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Goldschmidt-Clermont PJ, Khan A, Jimsheleishvili G, Graham P, Brooks A, Silvera R, Goldschmidt AJP, Pearse DD, Dietrich WD, Levi AD, Guest JD. Treating amyotrophic lateral sclerosis with allogeneic Schwann cell-derived exosomal vesicles: a case report. Neural Regen Res 2025; 20:1207-1216. [PMID: 38922880 DOI: 10.4103/nrr.nrr-d-23-01815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 02/24/2024] [Indexed: 06/28/2024] Open
Abstract
Schwann cells are essential for the maintenance and function of motor neurons, axonal networks, and the neuromuscular junction. In amyotrophic lateral sclerosis, where motor neuron function is progressively lost, Schwann cell function may also be impaired. Recently, important signaling and potential trophic activities of Schwann cell-derived exosomal vesicles have been reported. This case report describes the treatment of a patient with advanced amyotrophic lateral sclerosis using serial intravenous infusions of allogeneic Schwann cell-derived exosomal vesicles, marking, to our knowledge, the first instance of such treatment. An 81-year-old male patient presented with a 1.5-year history of rapidly progressive amyotrophic lateral sclerosis. After initial diagnosis, the patient underwent a combination of generic riluzole, sodium phenylbutyrate for the treatment of amyotrophic lateral sclerosis, and taurursodiol. The patient volunteered to participate in an FDA-approved single-patient expanded access treatment and received weekly intravenous infusions of allogeneic Schwann cell-derived exosomal vesicles to potentially restore impaired Schwann cell and motor neuron function. We confirmed that cultured Schwann cells obtained from the amyotrophic lateral sclerosis patient via sural nerve biopsy appeared impaired (senescent) and that exposure of the patient's Schwann cells to allogeneic Schwann cell-derived exosomal vesicles, cultured expanded from a cadaver donor improved their growth capacity in vitro. After a period of observation lasting 10 weeks, during which amyotrophic lateral sclerosis Functional Rating Scale-Revised and pulmonary function were regularly monitored, the patient received weekly consecutive infusions of 1.54 × 10 12 (×2), and then consecutive infusions of 7.5 × 10 12 (×6) allogeneic Schwann cell-derived exosomal vesicles diluted in 40 mL of Dulbecco's phosphate-buffered saline. None of the infusions were associated with adverse events such as infusion reactions (allergic or otherwise) or changes in vital signs. Clinical lab serum neurofilament and cytokine levels measured prior to each infusion varied somewhat without a clear trend. A more sensitive in-house assay suggested possible inflammasome activation during the disease course. A trend for clinical stabilization was observed during the infusion period. Our study provides a novel approach to address impaired Schwann cells and possibly motor neuron function in patients with amyotrophic lateral sclerosis using allogeneic Schwann cell-derived exosomal vesicles. Initial findings suggest that this approach is safe.
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Affiliation(s)
| | - Aisha Khan
- Stem Cell Institute, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - George Jimsheleishvili
- The Miami Project to Cure Paralysis, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Patricia Graham
- The Miami Project to Cure Paralysis, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Adriana Brooks
- The Miami Project to Cure Paralysis, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Risset Silvera
- The Miami Project to Cure Paralysis, Miller School of Medicine, University of Miami, Miami, FL, USA
| | | | - Damien D Pearse
- The Miami Project to Cure Paralysis, Miller School of Medicine, University of Miami, Miami, FL, USA
- Neurological Surgery, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - W Dalton Dietrich
- The Miami Project to Cure Paralysis, Miller School of Medicine, University of Miami, Miami, FL, USA
- Neurological Surgery, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Allan D Levi
- The Miami Project to Cure Paralysis, Miller School of Medicine, University of Miami, Miami, FL, USA
- Neurological Surgery, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - James D Guest
- The Miami Project to Cure Paralysis, Miller School of Medicine, University of Miami, Miami, FL, USA
- Neurological Surgery, Miller School of Medicine, University of Miami, Miami, FL, USA
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2
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Jiao D, Xu L, Gu Z, Yan H, Shen D, Gu X. Pathogenesis, diagnosis, and treatment of epilepsy: electromagnetic stimulation-mediated neuromodulation therapy and new technologies. Neural Regen Res 2025; 20:917-935. [PMID: 38989927 DOI: 10.4103/nrr.nrr-d-23-01444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/18/2024] [Indexed: 07/12/2024] Open
Abstract
Epilepsy is a severe, relapsing, and multifactorial neurological disorder. Studies regarding the accurate diagnosis, prognosis, and in-depth pathogenesis are crucial for the precise and effective treatment of epilepsy. The pathogenesis of epilepsy is complex and involves alterations in variables such as gene expression, protein expression, ion channel activity, energy metabolites, and gut microbiota composition. Satisfactory results are lacking for conventional treatments for epilepsy. Surgical resection of lesions, drug therapy, and non-drug interventions are mainly used in clinical practice to treat pain associated with epilepsy. Non-pharmacological treatments, such as a ketogenic diet, gene therapy for nerve regeneration, and neural regulation, are currently areas of research focus. This review provides a comprehensive overview of the pathogenesis, diagnostic methods, and treatments of epilepsy. It also elaborates on the theoretical basis, treatment modes, and effects of invasive nerve stimulation in neurotherapy, including percutaneous vagus nerve stimulation, deep brain electrical stimulation, repetitive nerve electrical stimulation, in addition to non-invasive transcranial magnetic stimulation and transcranial direct current stimulation. Numerous studies have shown that electromagnetic stimulation-mediated neuromodulation therapy can markedly improve neurological function and reduce the frequency of epileptic seizures. Additionally, many new technologies for the diagnosis and treatment of epilepsy are being explored. However, current research is mainly focused on analyzing patients' clinical manifestations and exploring relevant diagnostic and treatment methods to study the pathogenesis at a molecular level, which has led to a lack of consensus regarding the mechanisms related to the disease.
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Affiliation(s)
- Dian Jiao
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Lai Xu
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Zhen Gu
- Key Laboratory of Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Hua Yan
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Dingding Shen
- Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Xiaosong Gu
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
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3
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An Z, Jiang A, Chen J. Toward understanding the role of genomic repeat elements in neurodegenerative diseases. Neural Regen Res 2025; 20:646-659. [PMID: 38886931 DOI: 10.4103/nrr.nrr-d-23-01568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 03/02/2024] [Indexed: 06/20/2024] Open
Abstract
Neurodegenerative diseases cause great medical and economic burdens for both patients and society; however, the complex molecular mechanisms thereof are not yet well understood. With the development of high-coverage sequencing technology, researchers have started to notice that genomic repeat regions, previously neglected in search of disease culprits, are active contributors to multiple neurodegenerative diseases. In this review, we describe the association between repeat element variants and multiple degenerative diseases through genome-wide association studies and targeted sequencing. We discuss the identification of disease-relevant repeat element variants, further powered by the advancement of long-read sequencing technologies and their related tools, and summarize recent findings in the molecular mechanisms of repeat element variants in brain degeneration, such as those causing transcriptional silencing or RNA-mediated gain of toxic function. Furthermore, we describe how in silico predictions using innovative computational models, such as deep learning language models, could enhance and accelerate our understanding of the functional impact of repeat element variants. Finally, we discuss future directions to advance current findings for a better understanding of neurodegenerative diseases and the clinical applications of genomic repeat elements.
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Affiliation(s)
- Zhengyu An
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Aidi Jiang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Jingqi Chen
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Zhangjiang Fudan International Innovation Center, Shanghai, China
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4
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Hu Z, Yang J, Zhang S, Li M, Zuo C, Mao C, Zhang Z, Tang M, Shi C, Xu Y. AAV mediated carboxyl terminus of Hsp70 interacting protein overexpression mitigates the cognitive and pathological phenotypes of APP/PS1 mice. Neural Regen Res 2025; 20:253-264. [PMID: 38767490 PMCID: PMC11246129 DOI: 10.4103/nrr.nrr-d-23-01277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/27/2023] [Accepted: 01/02/2024] [Indexed: 05/22/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202501000-00033/figure1/v/2024-05-14T021156Z/r/image-tiff The E3 ubiquitin ligase, carboxyl terminus of heat shock protein 70 (Hsp70) interacting protein (CHIP), also functions as a co-chaperone and plays a crucial role in the protein quality control system. In this study, we aimed to investigate the neuroprotective effect of overexpressed CHIP on Alzheimer's disease. We used an adeno-associated virus vector that can cross the blood-brain barrier to mediate CHIP overexpression in APP/PS1 mouse brain. CHIP overexpression significantly ameliorated the performance of APP/PS1 mice in the Morris water maze and nest building tests, reduced amyloid-β plaques, and decreased the expression of both amyloid-β and phosphorylated tau. CHIP also alleviated the concentration of microglia and astrocytes around plaques. In APP/PS1 mice of a younger age, CHIP overexpression promoted an increase in ADAM10 expression and inhibited β-site APP cleaving enzyme 1, insulin degrading enzyme, and neprilysin expression. Levels of HSP70 and HSP40, which have functional relevance to CHIP, were also increased. Single nuclei transcriptome sequencing in the hippocampus of CHIP overexpressed mice showed that the lysosomal pathway and oligodendrocyte-related biological processes were up-regulated, which may also reflect a potential mechanism for the neuroprotective effect of CHIP. Our research shows that CHIP effectively reduces the behavior and pathological manifestations of APP/PS1 mice. Indeed, overexpression of CHIP could be a beneficial approach for the treatment of Alzheimer's disease.
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Affiliation(s)
- Zhengwei Hu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Academy of Medical Sciences of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Jing Yang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- NHC Key Laboratory of Prevention and treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Shuo Zhang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Academy of Medical Sciences of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Mengjie Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Chunyan Zuo
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Chengyuan Mao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- NHC Key Laboratory of Prevention and treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Zhongxian Zhang
- Sino-British Research Centre for Molecular Oncology, National Centre for International Research in Cell and Gene Therapy, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Mibo Tang
- Department of Gerontology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Changhe Shi
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- NHC Key Laboratory of Prevention and treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Yuming Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- NHC Key Laboratory of Prevention and treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, Henan Province, China
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5
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Wang Y, Ning X, Liang J, Wang A, Qu J. Enhancing microbial superoxide generation and conversion to hydroxyl radicals for enhanced bioremediation using iron-binding ligands. J Environ Sci (China) 2025; 147:597-606. [PMID: 39003074 DOI: 10.1016/j.jes.2023.11.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 07/15/2024]
Abstract
Harnessing bacteria for superoxide production in bioremediation holds immense promise, yet its practical application is hindered by slow production rates and the relatively weak redox potential of superoxide. This study delves into a cost-effective approach to amplify superoxide production using an Arthrobacter strain, a prevalent soil bacterial genus. Our research reveals that introducing a carbon source along with specific iron-binding ligands, including deferoxamine (DFO), diethylenetriamine pentaacetate (DTPA), citrate, and oxalate, robustly augments microbial superoxide generation. Moreover, our findings suggest that these iron-binding ligands play a pivotal role in converting superoxide into hydroxyl radicals by modulating the electron transfer rate between Fe(III)/Fe(II) and superoxide. Remarkably, among the tested ligands, only DTPA emerges as a potent promoter of this conversion process when complexed with Fe(III). We identify an optimal Fe(III) to DTPA ratio of approximately 1:1 for enhancing hydroxyl radical production within the Arthrobacter culture. This research underscores the efficacy of simultaneously introducing carbon sources and DTPA in facilitating superoxide production and its subsequent conversion to hydroxyl radicals, significantly elevating bioremediation performance. Furthermore, our study reveals that DTPA augments superoxide production in cultures of diverse soils, with various soil microorganisms beyond Arthrobacter identified as contributors to superoxide generation. This emphasizes the universal applicability of DTPA across multiple bacterial genera. In conclusion, our study introduces a promising methodology for enhancing microbial superoxide production and its conversion into hydroxyl radicals. These findings hold substantial implications for the deployment of microbial reactive oxygen species in bioremediation, offering innovative solutions for addressing environmental contamination challenges.
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Affiliation(s)
- Yuhan Wang
- School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Xue Ning
- SFI MaREI Centre for Energy, Climate and Marine, Environmental Research Institute, University College Cork, Cork, Ireland
| | - Jinsong Liang
- School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China.
| | - Aijie Wang
- School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Jiuhui Qu
- Center for Water and Ecology, Tsinghua University, Beijing 100084, China
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6
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Meng Q, Zhang Y, He D, Xia Y, Fu J, Dang C. Metagenomic perspectives on antibiotic resistance genes in tap water: The environmental characteristic, potential mobility and health threat. J Environ Sci (China) 2025; 147:582-596. [PMID: 39003073 DOI: 10.1016/j.jes.2023.12.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 12/23/2023] [Accepted: 12/24/2023] [Indexed: 07/15/2024]
Abstract
As an emerging environmental contaminant, antibiotic resistance genes (ARGs) in tap water have attracted great attention. Although studies have provided ARG profiles in tap water, research on their abundance levels, composition characteristics, and potential threat is still insufficient. Here, 9 household tap water samples were collected from the Guangdong-Hong Kong-Macao Greater Bay Area (GBA) in China. Additionally, 75 sets of environmental sample data (9 types) were downloaded from the public database. Metagenomics was then performed to explore the differences in the abundance and composition of ARGs. 221 ARG subtypes consisting of 17 types were detected in tap water. Although the ARG abundance in tap water was not significantly different from that found in drinking water plants and reservoirs, their composition varied. In tap water samples, the three most abundant classes of resistance genes were multidrug, fosfomycin and MLS (macrolide-lincosamide-streptogramin) ARGs, and their corresponding subtypes ompR, fosX and macB were also the most abundant ARG subtypes. Regarding the potential mobility, vanS had the highest abundance on plasmids and viruses, but the absence of key genes rendered resistance to vancomycin ineffective. Generally, the majority of ARGs present in tap water were those that have not been assessed and are currently not listed as high-threat level ARG families based on the World Health Organization Guideline. Although the current potential threat to human health posed by ARGs in tap water is limited, with persistent transfer and accumulation, especially in pathogens, the potential danger to human health posed by ARGs should not be ignored.
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Affiliation(s)
- Qiyue Meng
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yibo Zhang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Da He
- Key Laboratory of Ecological Impacts of Hydraulic Projects and Restoration of Aquatic Ecosystem of Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430074, China
| | - Yu Xia
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jie Fu
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Chenyuan Dang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
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7
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Xu X, Lin J, Wang J, Wang Y, Zhu Y, Wang J, Guo J. SPP1 expression indicates outcome of immunotherapy plus tyrosine kinase inhibition in advanced renal cell carcinoma. Hum Vaccin Immunother 2024; 20:2350101. [PMID: 38738709 PMCID: PMC11093034 DOI: 10.1080/21645515.2024.2350101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/28/2024] [Indexed: 05/14/2024] Open
Abstract
Clinical guidelines have recently advised combination therapy involving immunotherapy (IO) and tyrosine kinase inhibitors (TKI) as the first-line therapy approach for advanced renal cell carcinoma (RCC). Nevertheless, there is currently no available biomarker that can effectively distinguish the progression-free survival (PFS). RNA-sequencing and immunohistochemistry were conducted on our cohort of metastatic RCC patients, namely ZS-MRCC, who received combination therapy consisting of IO and TKI. We further applied RNA-sequencing, immunohistochemistry, and flow cytometry to examine the immune cell infiltration and functionality inside the tumor microenvironment of high-risk localized RCC samples. SPP1 expression was significantly higher in non-responders to IO-TKI therapy. Elevated levels of SPP1 were associated with poor PFS in both the ZS-MRCC cohort (HR = 2.73, p = .018) and validated in the JAVELIN Renal 101 cohort (HR = 1.61, p = .004). By multivariate Cox analysis, SPP1 was identified as a significant independent prognosticator. Furthermore, there existed a negative correlation between elevated levels of SPP1 and the presence of GZMB+CD8+ T cells (Spearman's ρ= -0.48, p < .001). Conversely, SPP1 expression is associated with T cell exhaustion markers. A significant increase in the abundance of Tregs was observed in tumors with high levels of SPP1. Additionally, a machine-learning-based model was constructed to predict the benefit of IO-TKI treatment. High SPP1 is associated with therapeutic resistance and unfavorable PFS in IO-TKI therapy. SPP1 expression have also been observed to be indicative of malfunction and exhaustion in T cells. Increased SPP1 expression has the potential to serve as a potential biomarker for treatment selection of metastatic RCC.
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Affiliation(s)
- Xianglai Xu
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Urology, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
- Xiamen Clinical Research Center for Cancer Therapy, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
| | - Jinglai Lin
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Urology, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
- Xiamen Clinical Research Center for Cancer Therapy, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
| | - Jiahao Wang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ying Wang
- Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yanjun Zhu
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jiajun Wang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianming Guo
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
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8
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van Allen KA, Gang N, Hoyeck MP, Perera I, Zhang D, Atlas E, Lynn FC, Bruin JE. Characterizing the effects of Dechlorane Plus on β-cells: a comparative study across models and species. Islets 2024; 16:2361996. [PMID: 38833523 DOI: 10.1080/19382014.2024.2361996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 05/27/2024] [Indexed: 06/06/2024] Open
Abstract
Epidemiological studies consistently link environmental toxicant exposure with increased Type 2 diabetes risk. Our study investigated the diabetogenic effects of a widely used flame retardant, Dechlorane Plus (DP), on pancreatic β-cells using rodent and human model systems. We first examined pancreas tissues from male mice exposed daily to oral gavage of either vehicle (corn oil) or DP (10, 100, or 1000 μg/kg per day) and fed chow or high fat diet for 28-days in vivo. DP exposure did not affect islet size or endocrine cell composition in either diet group. Next, we assessed the effect of 48-hour exposure to vehicle (DMSO) or DP (1, 10, or 100 nM) in vitro using immortalized rat β-cells (INS-1 832/3), primary mouse and human islets, and human stem-cell derived islet-like cells (SC-islets). In INS-1 832/3 cells, DP did not impact glucose-stimulated insulin secretion (GSIS) but significantly decreased intracellular insulin content. DP had no effect on GSIS in mouse islets or SC-islets but had variable effects on GSIS in human islets depending on the donor. DP alone did not affect insulin content in mouse islets, human islets, or SC-islets, but mouse islets co-exposed to DP and glucolipotoxic (GLT) stress conditions (28.7 mM glucose + 0.5 mM palmitate) had reduced insulin content compared to control conditions. Co-exposure of mouse islets to DP + GLT amplified the upregulation of Slc30a8 compared to GLT alone. Our study highlights the importance and challenges of using different in vitro models for studying chemical toxicity.
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Affiliation(s)
- Kyle A van Allen
- Department of Biology & Institute of Biochemistry, Carleton University, Ottawa, Ontario, Canada
| | - Noa Gang
- Department of Biology & Institute of Biochemistry, Carleton University, Ottawa, Ontario, Canada
- Diabetes Research Group, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Myriam P Hoyeck
- Department of Biology & Institute of Biochemistry, Carleton University, Ottawa, Ontario, Canada
| | - Ineli Perera
- Department of Biology & Institute of Biochemistry, Carleton University, Ottawa, Ontario, Canada
| | - Dahai Zhang
- Diabetes Research Group, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Ella Atlas
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | - Francis C Lynn
- Diabetes Research Group, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Jennifer E Bruin
- Department of Biology & Institute of Biochemistry, Carleton University, Ottawa, Ontario, Canada
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9
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Cargnin Faccin F, Perez DR. Pandemic preparedness through vaccine development for avian influenza viruses. Hum Vaccin Immunother 2024; 20:2347019. [PMID: 38807261 PMCID: PMC11141480 DOI: 10.1080/21645515.2024.2347019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/22/2024] [Indexed: 05/30/2024] Open
Abstract
Influenza A viruses pose a significant threat to global health, impacting both humans and animals. Zoonotic transmission, particularly from swine and avian species, is the primary source of human influenza outbreaks. Notably, avian influenza viruses of the H5N1, H7N9, and H9N2 subtypes are of pandemic concern through their global spread and sporadic human infections. Preventing and controlling these viruses is critical due to their high threat level. Vaccination remains the most effective strategy for influenza prevention and control in humans, despite varying vaccine efficacy across strains. This review focuses specifically on pandemic preparedness for avian influenza viruses. We delve into vaccines tested in animal models and summarize clinical trials conducted on H5N1, H7N9, and H9N2 vaccines in humans.
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Affiliation(s)
- Flavio Cargnin Faccin
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Daniel R. Perez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
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10
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Huang Q, Li H, Zhang Y. A bibliometric and knowledge-map study on the treatment of hematological malignancies with CAR-T cells from 2012 to 2023. Hum Vaccin Immunother 2024; 20:2371664. [PMID: 38961667 PMCID: PMC11225924 DOI: 10.1080/21645515.2024.2371664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/20/2024] [Indexed: 07/05/2024] Open
Abstract
Recently, CAR-T cell therapy in hematological malignancies has received extensive attention. The objective of this study is to gain a comprehensive understanding of the current research status, development trends, research hotspots, and emerging topics pertaining to CAR-T cells in the treatment of hematological malignancies. Articles pertaining to CAR-T cell therapy for hematological malignancies from the years 2012 to 2023 were obtained and assessed from the Web of Science Core Collection (WoSCC). A bibliometric approach was employed to conduct a scientific, comprehensive, and objective quantitative analysis, as well as a visual analysis, of this particular research domain. A comprehensive analysis was conducted on a corpus of 3643 articles, which were collaboratively authored by 72 countries and various research institutions. CAR-T cell research in treating hematological malignancies shows an increasing trend each year. Notably, the study identified the countries and institutions displaying the highest level of activity, the journals with the most citations and output, as well as the authors who garnered the highest frequency of citations and co-citations. Furthermore, the analysis successfully identified the research hotspots and highlighted six emerging topics within this domain. This study conducted a comprehensive exploration and analysis of the research status, development trends, research hotspots, and emerging topics about CAR-T cells in the treatment of hematological malignancies from 2012 to 2023. The findings of this study will serve as a valuable reference and guide for researchers seeking to delve deeper into this field and determine the future direction of their research.
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Affiliation(s)
- Qing Huang
- Department of Hematology, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Huimin Li
- Department of Hematology, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Yuan Zhang
- Department of Hematology, The Fifth Medical Center of PLA General Hospital, Beijing, China
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11
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Huang Y, Chen Z, Shen G, Fang S, Zheng J, Chi Z, Zhang Y, Zou Y, Gan Q, Liao C, Yao Y, Kong J, Fan X. Immune regulation and the tumor microenvironment in anti-PD-1/PDL-1 and anti-CTLA-4 therapies for cancer immune evasion: A bibliometric analysis. Hum Vaccin Immunother 2024; 20:2318815. [PMID: 38419524 DOI: 10.1080/21645515.2024.2318815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/11/2024] [Indexed: 03/02/2024] Open
Abstract
This study aims to conduct a bibliometric analysis, employing visualization tools to examine literature pertaining to tumor immune evasion related to anti-CTLA-4 and anti-PD-1/PD-L1 therapy from 1999 to 2022. A special emphasis is placed on the interplay between tumor microenvironment, signaling pathways, immune cells and immune evasion, with data sourced from the Web of Science core collection (WoSCC). Advanced tools, including VOSviewer, Citespace, and Scimago Graphica, were utilized to analyze various parameters, such as co-authorship/co-citation patterns, regional contributions, journal preferences, keyword co-occurrences, and significant citation bursts. Out of 4778 publications reviewed, there was a marked increase in research focusing on immune evasion, with bladder cancer being notably prominent. Geographically, China, the USA, and Japan were the leading contributors. Prestigious institutions like MD Anderson Cancer Center, Harvard Medical School, Fudan University, and Sun Yat Sen University emerged as major players. Renowned journals in this domain included Frontiers in Immunology, Cancers, and Frontiers in Oncology. Ehen LP and Wang W were identified as prolific authors on this topic, while Topalian SL stood out as one of the most cited. Research current situation is notably pivoting toward challenges like immunotherapy resistance and the intricate signaling pathways driving drug resistance. This bibliometric study seeks to provide a comprehensive overview of past and current research trends, emphasizing the potential role of tumor microenvironment, signaling pathways and immune cells in the context of immune checkpoint inhibitors (ICIs) and tumor immune evasion.
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Affiliation(s)
- Yi Huang
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Clinical Research Center for Urological Diseases, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Zhijian Chen
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Clinical Research Center for Urological Diseases, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Gang Shen
- Department of Urology, DUSHU Lake Hospital Affiliated to Soochow University, Suzhou, China
| | - Shuogui Fang
- Department of Radiotherapy, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
| | - Junjiong Zheng
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Clinical Research Center for Urological Diseases, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Zepai Chi
- Department of urology, Shantou Central Hospital, Shantou, China
| | - Yuanfeng Zhang
- Department of urology, Shantou Central Hospital, Shantou, China
| | - Yitong Zou
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Clinical Research Center for Urological Diseases, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Qinghua Gan
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Clinical Research Center for Urological Diseases, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Chengxiao Liao
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Clinical Research Center for Urological Diseases, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Yuhui Yao
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Clinical Research Center for Urological Diseases, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Jianqiu Kong
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Clinical Research Center for Urological Diseases, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Xinxiang Fan
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Clinical Research Center for Urological Diseases, Sun Yat-Sen University, Guangzhou, P. R. China
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12
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Mihaylova NM, Manoylov IK, Nikolova MH, Prechl J, Tchorbanov AI. DNA and protein-generated chimeric molecules for delivery of influenza viral epitopes in mouse and humanized NSG transfer models. Hum Vaccin Immunother 2024; 20:2292381. [PMID: 38193304 DOI: 10.1080/21645515.2023.2292381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 12/05/2023] [Indexed: 01/10/2024] Open
Abstract
Purified subunit viral antigens are weakly immunogenic and stimulate only the antibody but not the T cell-mediated immune response. An alternative approach to inducing protective immunity with small viral peptides may be the targeting of viral epitopes to immunocompetent cells by DNA and protein-engineered vaccines. This review will focus on DNA and protein-generated chimeric molecules carrying engineered fragments specific for activating cell surface co-receptors for inducing protective antiviral immunity. Adjuvanted protein-based vaccine or DNA constructs encoding simultaneously T- and B-cell peptide epitopes from influenza viral hemagglutinin, and scFvs specific for costimulatory immune cell receptors may induce a significant increase of anti-influenza antibody levels and strong CTL activity against virus-infected cells in a manner that mimics the natural infection. Here we summarize the development of several DNA and protein chimeric constructs carrying influenza virus HA317-41 fragment. The generated engineered molecules were used for immunization in intact murine and experimentally humanized NSG mouse models.
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Affiliation(s)
- Nikolina M Mihaylova
- Laboratory of Experimental Immunology, Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Iliyan K Manoylov
- Laboratory of Experimental Immunology, Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Maria H Nikolova
- National Reference Laboratory of Immunology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - Andrey I Tchorbanov
- Laboratory of Experimental Immunology, Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
- National Institute of Immunology, Sofia, Bulgaria
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13
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Xin K, Wei X, Shao J, Chen F, Liu Q, Liu B. Establishment of a novel tumor neoantigen prediction tool for personalized vaccine design. Hum Vaccin Immunother 2024; 20:2300881. [PMID: 38214336 DOI: 10.1080/21645515.2023.2300881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/28/2023] [Indexed: 01/13/2024] Open
Abstract
The personalized neoantigen nanovaccine (PNVAC) platform for patients with gastric cancer we established previously exhibited promising anti-tumor immunoreaction. However, limited by the ability of traditional neoantigen prediction tools, a portion of epitopes failed to induce specific immune response. In order to filter out more neoantigens to optimize our PNVAC platform, we develop a novel neoantigen prediction model, NUCC. This prediction tool trained through a deep learning approach exhibits better neoantigen prediction performance than other prediction tools, not only in two independent epitope datasets, but also in a totally new epitope dataset we construct from scratch, including 25 patients with advance gastric cancer and 150 candidate mutant peptides, 13 of which prove to be neoantigen by immunogenicity test in vitro. Our work lay the foundation for the improvement of our PNVAC platform for gastric cancer in the future.
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Affiliation(s)
- Kai Xin
- Department of Oncology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, China
| | - Xiao Wei
- Department of Pathology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, China
| | - Jie Shao
- Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, China
| | - Fangjun Chen
- Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, China
| | - Qin Liu
- Department of Oncology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, China
- Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, China
| | - Baorui Liu
- Department of Oncology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, China
- Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, China
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Ahrberg Y, Dallmann J, Freitag J, Hassan A, Jung C, Kiefer J, Muralidharan AM, Peter M, Beck JD. CIMT 2024: Report on the 21st Annual Meeting of the Association for Cancer Immunotherapy. Hum Vaccin Immunother 2024; 20:2381925. [PMID: 39043196 PMCID: PMC11268217 DOI: 10.1080/21645515.2024.2381925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 07/16/2024] [Indexed: 07/25/2024] Open
Abstract
The 21st Association for Cancer Immunotherapy (CIMT) Annual Meeting took place from May 15th to May 17th in Mainz, Germany, and was attended by a total of 855 academic and clinical professionals hailing from 33 different countries. The conference served as a platform for these experts to convene and discuss the latest breakthroughs in cancer immunology and immunotherapy research. Dedicated sessions covering advancements in artificial intelligence tools for cancer immunotherapy research, as well as the landscape of cancer care and cancer immunotherapy trials on the African continent, prompted lively and informative discussions among the attendees. This report aims to provide an overview of the most noteworthy highlights and key takeaways from CIMT2024.
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Affiliation(s)
- Yasemin Ahrberg
- TRON-Translational Oncology, University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz, Germany
| | | | - Janina Freitag
- TRON-Translational Oncology, University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz, Germany
| | | | | | | | - Anindhita Meena Muralidharan
- TRON-Translational Oncology, University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz, Germany
| | - Matthias Peter
- TRON-Translational Oncology, University Medical Center of Johannes Gutenberg University Mainz gGmbH, Mainz, Germany
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15
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O’Neill BF, Boeckman C, LeRoy K, Linderblood C, Olson T, Woods R, Challender M. An environmental risk assessment of IPD079Ea: a protein derived from Ophioglossum pendulum with activity against Diabrotica spp.In maize. GM CROPS & FOOD 2024; 15:15-31. [PMID: 38238889 PMCID: PMC10802193 DOI: 10.1080/21645698.2023.2299503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/21/2023] [Indexed: 01/23/2024]
Abstract
Farmers in North America face significant pressure from insects in their maize fields, particularly from corn rootworm (Diabrotica spp.). Research into proteins capable of insecticidal activity has found several produced by ferns. One protein, IPD079Ea, was derived from Ophioglossum pendulum and has shown activity against corn rootworm. An environmental risk assessment was conducted for maize event DP-915635-4, which provides control of corn rootworms via expression of the IPD079Ea protein. This assessment focused on IPD079Ea and characterized potential exposure and hazard to non-target organisms (NTOs). For exposure, estimated environmental concentrations (EECs) were calculated. For hazard, laboratory dietary toxicity studies were conducted with IPD079Ea and surrogate non-target organisms. Environmental risk was characterized by comparing hazard and exposure to calculate the margin of exposure (MOE). Based on the MOE values for DP-915635-4 maize, the IPD079Ea protein is not expected to result in unreasonable adverse effects on beneficial NTO populations at environmentally relevant concentrations.
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Affiliation(s)
- Bridget F. O’Neill
- Corteva Agriscience™, Regulatory and Stewardship institution, Indianapolis, IN, USA
| | - Chad Boeckman
- Corteva Agriscience™, Regulatory and Stewardship, Johnston, IA, USA
| | - Kristine LeRoy
- Corteva Agriscience™, Regulatory and Stewardship, Johnston, IA, USA
| | | | - Taylor Olson
- Corteva Agriscience™, Regulatory and Stewardship, Johnston, IA, USA
| | - Rachel Woods
- Corteva Agriscience™, Regulatory and Stewardship, Johnston, IA, USA
| | - Mary Challender
- Corteva Agriscience™, Regulatory and Stewardship, Johnston, IA, USA
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16
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Yang L, Yang X, Shen B, Jin J, Li L, Fan D, Xiaokelaiti S, Hao Q, Niu J. Effects of high-temperature stress on gene expression related to photosynthesis in two jujube ( Ziziphus jujuba Mill.) varieties. PLANT SIGNALING & BEHAVIOR 2024; 19:2357367. [PMID: 38775124 PMCID: PMC11139005 DOI: 10.1080/15592324.2024.2357367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/08/2024] [Indexed: 06/01/2024]
Abstract
Elevated temperatures critically impact crop growth, development, and yield, with photosynthesis being the most temperature-sensitive physiological process in plants. This study focused on assessing the photosynthetic response and genetic adaptation of two different heat-resistant jujube varieties 'Junzao' (J) and 'Fucuimi' (F), to high-temperature stress (42°C Day/30°C Night). Comparative analyses of leaf photosynthetic indices, microstructural changes, and transcriptome sequencing were conducted. Results indicated superior high-temperature adaptability in F, evidenced by alterations in leaf stomatal behavior - particularly in J, where defense cells exhibited significant water loss, shrinkage, and reduced stomatal opening, alongside a marked increase in stomatal density. Through transcriptome sequencing 13,884 differentially expressed genes (DEGs) were identified, significantly enriched in pathways related to plant-pathogen interactions, amino acid biosynthesis, starch and sucrose metabolism, and carbohydrate metabolism. Key findings include the identification of photosynthetic pathway related DEGs and HSFA1s as central regulators of thermal morphogenesis and heat stress response. Revealing their upregulation in F and downregulation in J. The results indicate that these genes play a crucial role in improving heat tolerance in F. This study unveils critical photosynthetic genes involved in heat stress, providing a theoretical foundation for comprehending the molecular mechanisms underlying jujube heat tolerance.
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Affiliation(s)
- Lei Yang
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, Xinjiang, China
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Scientific Observing and Experimental Station of Pomology (Xinjiang), Urumqi, Xinjiang, China
| | - Xiaojuan Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Scientific Observing and Experimental Station of Pomology (Xinjiang), Urumqi, Xinjiang, China
| | - Bingqi Shen
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Scientific Observing and Experimental Station of Pomology (Xinjiang), Urumqi, Xinjiang, China
| | - Juan Jin
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Scientific Observing and Experimental Station of Pomology (Xinjiang), Urumqi, Xinjiang, China
| | - Lili Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Scientific Observing and Experimental Station of Pomology (Xinjiang), Urumqi, Xinjiang, China
| | - Dingyu Fan
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Scientific Observing and Experimental Station of Pomology (Xinjiang), Urumqi, Xinjiang, China
| | - Subina Xiaokelaiti
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Scientific Observing and Experimental Station of Pomology (Xinjiang), Urumqi, Xinjiang, China
| | - Qing Hao
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Scientific Observing and Experimental Station of Pomology (Xinjiang), Urumqi, Xinjiang, China
| | - Jianxin Niu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, Xinjiang, China
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Jeon D, Hill E, McNeel DG. Toll-like receptor agonists as cancer vaccine adjuvants. Hum Vaccin Immunother 2024; 20:2297453. [PMID: 38155525 PMCID: PMC10760790 DOI: 10.1080/21645515.2023.2297453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/16/2023] [Indexed: 12/30/2023] Open
Abstract
Cancer immunotherapy has emerged as a promising strategy to treat cancer patients. Among the wide range of immunological approaches, cancer vaccines have been investigated to activate and expand tumor-reactive T cells. However, most cancer vaccines have not shown significant clinical benefit as monotherapies. This is likely due to the antigen targets of vaccines, "self" proteins to which there is tolerance, as well as to the immunosuppressive tumor microenvironment. To help circumvent immune tolerance and generate effective immune responses, adjuvants for cancer vaccines are necessary. One representative adjuvant family is Toll-Like receptor (TLR) agonists, synthetic molecules that stimulate TLRs. TLRs are the largest family of pattern recognition receptors (PRRs) that serve as the sensors of pathogens or cellular damage. They recognize conserved foreign molecules from pathogens or internal molecules from cellular damage and propel innate immune responses. When used with vaccines, activation of TLRs signals an innate damage response that can facilitate the development of a strong adaptive immune response against the target antigen. The ability of TLR agonists to modulate innate immune responses has positioned them to serve as adjuvants for vaccines targeting infectious diseases and cancers. This review provides a summary of various TLRs, including their expression patterns, their functions in the immune system, as well as their ligands and synthetic molecules developed as TLR agonists. In addition, it presents a comprehensive overview of recent strategies employing different TLR agonists as adjuvants in cancer vaccine development, both in pre-clinical models and ongoing clinical trials.
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Affiliation(s)
- Donghwan Jeon
- Department of Oncology, University of Wisconsin Carbone Cancer Center, Madison, WI, USA
| | - Ethan Hill
- Department of Medicine, University of Wisconsin Carbone Cancer Center, Madison, WI, USA
| | - Douglas G. McNeel
- Department of Medicine, University of Wisconsin Carbone Cancer Center, Madison, WI, USA
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Aparicio B, Theunissen P, Hervas-Stubbs S, Fortes P, Sarobe P. Relevance of mutation-derived neoantigens and non-classical antigens for anticancer therapies. Hum Vaccin Immunother 2024; 20:2303799. [PMID: 38346926 PMCID: PMC10863374 DOI: 10.1080/21645515.2024.2303799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/06/2024] [Indexed: 02/15/2024] Open
Abstract
Efficacy of cancer immunotherapies relies on correct recognition of tumor antigens by lymphocytes, eliciting thus functional responses capable of eliminating tumor cells. Therefore, important efforts have been carried out in antigen identification, with the aim of understanding mechanisms of response to immunotherapy and to design safer and more efficient strategies. In addition to classical tumor-associated antigens identified during the last decades, implementation of next-generation sequencing methodologies is enabling the identification of neoantigens (neoAgs) arising from mutations, leading to the development of new neoAg-directed therapies. Moreover, there are numerous non-classical tumor antigens originated from other sources and identified by new methodologies. Here, we review the relevance of neoAgs in different immunotherapies and the results obtained by applying neoAg-based strategies. In addition, the different types of non-classical tumor antigens and the best approaches for their identification are described. This will help to increase the spectrum of targetable molecules useful in cancer immunotherapies.
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Affiliation(s)
- Belen Aparicio
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Patrick Theunissen
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Sandra Hervas-Stubbs
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Puri Fortes
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Spanish Network for Advanced Therapies (TERAV ISCIII), Spain
| | - Pablo Sarobe
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
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19
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Li T, Jia W, Peng S, Guo Y, Liu J, Zhang X, Li P, Zhang H, Xu R. Endogenous cAMP elevation in Brassica napus causes changes in phytohormone levels. PLANT SIGNALING & BEHAVIOR 2024; 19:2310963. [PMID: 38314783 PMCID: PMC10854363 DOI: 10.1080/15592324.2024.2310963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/22/2024] [Indexed: 02/07/2024]
Abstract
In higher plants, the regulatory roles of cAMP (cyclic adenosine 3',5'-monophosphate) signaling remain elusive until now. Cellular cAMP levels are generally much lower in higher plants than in animals and transiently elevated for triggering downstream signaling events. Moreover, plant adenylate cyclase (AC) activities are found in different moonlighting multifunctional proteins, which may pose additional complications in distinguishing a specific signaling role for cAMP. Here, we have developed rapeseed (Brassica napus L.) transgenic plants that overexpress an inducible plant-origin AC activity for generating high AC levels much like that in animal cells, which served the genetic model disturbing native cAMP signaling as a whole in plants. We found that overexpression of the soluble AC activity had significant impacts on the contents of indole-3-acetic acid (IAA) and stress phytohormones, i.e. jasmonic acid (JA), abscisic acid (ABA), and salicylic acid (SA) in the transgenic plants. Acute induction of the AC activity caused IAA overaccumulation, and upregulation of TAA1 and CYP83B1 in the IAA biosynthesis pathways, but also simultaneously the hyper-induction of PR4 and KIN2 expression indicating activation of JA and ABA signaling pathways. We observed typical overgrowth phenotypes related to IAA excess in the transgenic plants, including significant increases in plant height, internode length, width of leaf blade, petiole length, root length, and fresh shoot biomass, as well as the precocious seed development, as compared to wild-type plants. In addition, we identified a set of 1465 cAMP-responsive genes (CRGs), which are most significantly enriched in plant hormone signal transduction pathway, and function mainly in relevance to hormonal, abiotic and biotic stress responses, as well as growth and development. Collectively, our results support that cAMP elevation impacts phytohormone homeostasis and signaling, and modulates plant growth and development. We proposed that cAMP signaling may be critical in configuring the coordinated regulation of growth and development in higher plants.
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Affiliation(s)
- Tianming Li
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wenjing Jia
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Song Peng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Yanhui Guo
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Jinrui Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Xue Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Panyu Li
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Hanfeng Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Ruqiang Xu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
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20
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Li D, Li H, Feng H, Qi P, Wu Z. Unveiling kiwifruit TCP genes: evolution, functions, and expression insights. PLANT SIGNALING & BEHAVIOR 2024; 19:2338985. [PMID: 38597293 PMCID: PMC11008546 DOI: 10.1080/15592324.2024.2338985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 03/26/2024] [Indexed: 04/11/2024]
Abstract
The TEOSINTE-BRANCHED1/CYCLOIDEA/PROLEFERATING-CELL-FACTORS (TCP) gene family is a plant-specific transcriptional factor family involved in leaf morphogenesis and senescence, lateral branching, hormone crosstalk, and stress responses. To date, a systematic study on the identification and characterization of the TCP gene family in kiwifruit has not been reported. Additionally, the function of kiwifruit TCPs in regulating kiwifruit responses to the ethylene treatment and bacterial canker disease pathogen (Pseudomonas syringae pv. actinidiae, Psa) has not been investigated. Here, we identified 40 and 26 TCP genes in Actinidia chinensis (Ac) and A. eriantha (Ae) genomes, respectively. The synteny analysis of AcTCPs illustrated that whole-genome duplication accounted for the expansion of the TCP family in Ac. Phylogenetic, conserved domain, and selection pressure analysis indicated that TCP family genes in Ac and Ae had undergone different evolutionary patterns after whole-genome duplication (WGD) events, causing differences in TCP gene number and distribution. Our results also suggested that protein structure and cis-element architecture in promoter regions of TCP genes have driven the function divergence of duplicated gene pairs. Three and four AcTCP genes significantly affected kiwifruit responses to the ethylene treatment and Psa invasion, respectively. Our results provided insight into general characters, evolutionary patterns, and functional diversity of kiwifruit TCPs.
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Affiliation(s)
- Donglin Li
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Haibo Li
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Huimin Feng
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Ping Qi
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Zhicheng Wu
- College of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
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21
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Zhang K, Zheng X, Sun Y, Feng X, Wu X, Liu W, Gao C, Yan Y, Tian W, Wang Y. TOP2A modulates signaling via the AKT/mTOR pathway to promote ovarian cancer cell proliferation. Cancer Biol Ther 2024; 25:2325126. [PMID: 38445610 PMCID: PMC10936659 DOI: 10.1080/15384047.2024.2325126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/26/2024] [Indexed: 03/07/2024] Open
Abstract
Ovarian cancer (OC) is a form of gynecological malignancy that is associated with worse patient outcomes than any other cancer of the female reproductive tract. Topoisomerase II α (TOP2A) is commonly regarded as an oncogene that is associated with malignant disease progression in a variety of cancers, its mechanistic functions in OC have yet to be firmly established. We explored the role of TOP2A in OC through online databases, clinical samples, in vitro and in vivo experiments. And initial analyses of public databases revealed high OC-related TOP2A expression in patient samples that was related to poorer prognosis. This was confirmed by clinical samples in which TOP2A expression was elevated in OC relative to healthy tissue. Kaplan-Meier analyses further suggested that higher TOP2A expression levels were correlated with worse prognosis in OC patients. In vitro, TOP2A knockdown resulted in the inhibition of OC cell proliferation, with cells entering G1 phase arrest and undergoing consequent apoptotic death. In rescue assays, TOP2A was confirmed to regulate cell proliferation and cell cycle through AKT/mTOR pathway activity. Mouse model experiments further affirmed the key role that TOP2A plays as a driver of OC cell proliferation. These data provide strong evidence supporting TOP2A as an oncogenic mediator and prognostic biomarker related to OC progression and poor outcomes. At the mechanistic level, TOP2A can control tumor cell growth via AKT/mTOR pathway modulation. These preliminary results provide a foundation for future research seeking to explore the utility of TOP2A inhibitor-based combination treatment regimens in platinum-resistant recurrent OC patients.
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Affiliation(s)
- Kaiwen Zhang
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China
| | - Xingyu Zheng
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China
| | - Yiqing Sun
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China
| | - Xinyu Feng
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China
| | - Xirong Wu
- Department of Gynecology and Obstetrics, Affiliated Hospital of Nantong University, Nantong, China
| | - Wenlu Liu
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China
| | - Chao Gao
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China
| | - Ye Yan
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China
| | - Wenyan Tian
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China
| | - Yingmei Wang
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China
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22
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Zhao X, Gao Q, Wang H, Yue J, An D, Li B, Yan F, Carmen SM, Zhao Y, Zhou H, Zhao M. syn-tasiRnas targeting the coat protein of potato virus Y confer antiviral resistance in Nicotiana benthamiana. PLANT SIGNALING & BEHAVIOR 2024; 19:2358270. [PMID: 38796845 PMCID: PMC11135832 DOI: 10.1080/15592324.2024.2358270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024]
Abstract
Trans-acting small interfering RNAs (tasiRNAs) are 21-nt phased (phased siRNAs) resulting from successive DCL-catalyzed processing from the end of a double-stranded RNA substrate originating from the RDR of an AGO-catalyzed cleaved RNA at a micro RNA target site. Plant tasiRNAs have been synthesized to produce synthetic tasiRNAs (syn-tasiRNAs) targeting viral RNAs that confer viral resistance. In this study, we engineered syn-tasiRNAs to target potato virus Y (PVY) infection by replacing five native siRNAs of TAS1c with 210-bp fragments from the coat protein (CP) region of the PVY genome. The results showed that the transient expression of syn-tasiR-CPpvy2 in Nicotiana benthamiana (N. benthamiana) plants conferred antiviral resistance, supported by the absence of PVY infection symptoms and viral accumulation. This indicated that syn-tasiR-CPpvy2 successfully targeted and silenced the PVY CP gene, effectively inhibiting viral infection. syn-tasiR-CPpvy1 displayed attenuated symptoms and decreased viral accumulation in these plants However, severe symptoms of PVY infection and a similar amount of viral accumulation as the control were observed in plants expressing syn-tasiR-CPpvy3. syn-tasiR-CPpvy/pvx, which targets both PVY and potato virus X (PVX), was engineered using a single precursor. After the transient expression of syn-tasiR-CPpvy/pvx3 and syn-tasiR-CPpvy/pvx5 in N. benthamiana, the plants were resistant to both PVY and PVX. These results suggested that engineered syn-tasiRNAs could not only specifically induce antiviral resistance against one target virus but could also be designed for multi-targeted silencing of different viruses, thereby preventing complex virus infection in plants.
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Affiliation(s)
- Xingyue Zhao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Qian Gao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Haijuan Wang
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Jianying Yue
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Derong An
- College of Plant Protection, Northwest A&F University, Yangling, China
| | - Bin Li
- Department of Tabacco Production, Sichuan Province Company of Tobacco Corporation in China, Chengdu, China
| | - Fangfang Yan
- Panzhihua City company of Sichuan province company of Tobacco Corporation in China, Panzhihua city, Sichuan provience, China
| | | | - Yuanzheng Zhao
- Department of Plant Protection, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Hongyou Zhou
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Mingmin Zhao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
- Department of Plant protection, Key Laboratory of the Development and Resource Utilization of Biological Pesticide in Inner Mongolia, Hohhot, China
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23
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Brookes G, Smyth SJ. Risk-appropriate regulations for gene-editing technologies. GM CROPS & FOOD 2024; 15:1-14. [PMID: 38215017 DOI: 10.1080/21645698.2023.2293510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/07/2023] [Indexed: 01/14/2024]
Abstract
This paper explores the scope for the newly emerging technologies, based on gene editing (GE) contributing to addressing the global challenges that we face. These challenges relate to food security, climate change and biodiversity depletion. In particular, it examines the science and evidence behind the most appropriate forms of agricultural production to meet these challenges, the targets set in the Global Biodiversity Framework (GBF) agreed to at the end of 2022 and the possible role of GE technologies in contributing to meeting these targets. It then examines the most risk-appropriate regulatory environment required to best facilitate the adoption of GE technology, drawing on the experiences of the impact of regulatory systems for other innovations used in agricultural and food production systems such as genetically modified organisms (GMOs).
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Affiliation(s)
| | - Stuart J Smyth
- College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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24
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Yang L, Wang Q, He L, Sun X. The critical role of tumor microbiome in cancer immunotherapy. Cancer Biol Ther 2024; 25:2301801. [PMID: 38241173 PMCID: PMC10802201 DOI: 10.1080/15384047.2024.2301801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/01/2024] [Indexed: 01/21/2024] Open
Abstract
In recent years, the microbiome has shown an integral role in cancer immunotherapy and has become a prominent and widely studied topic. A full understanding of the interactions between the tumor microbiome and various immunotherapies offers opportunities for immunotherapy of cancer. This review scrutinizes the composition of the tumor microbiome, the mechanism of microbial immune regulation, the influence of tumor microorganisms on tumor metastasis, and the interaction between tumor microorganisms and immunotherapy. In addition, this review also summarizes the challenges and opportunities of immunotherapy through tumor microbes, as well as the prospects and directions for future related research. In conclusion, the potential of microbial immunotherapy to enhance treatment outcomes for cancer patients should not be underestimated. Through this review, it is hoped that more research on tumor microbial immunotherapy will be done to better solve the treatment problems of cancer patients.
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Affiliation(s)
- Liu Yang
- School of Clinical Medicine, The Affiliated Hospital, Southwest Medical University, Luzhou, China
| | - Qi Wang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Lijuan He
- Department of Health Management Center, The Affiliated Hospital, Southwest Medical University, Luzhou, China
| | - Xingyu Sun
- Department of Gynecology, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China
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25
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Chege P, Njagi J, Komen J, Ngure G, Muriuki J, Karembu M. Best practices for acceptability of GM crops field trials conclusions: lessons for Africa. GM CROPS & FOOD 2024; 15:222-232. [PMID: 38980826 PMCID: PMC11236291 DOI: 10.1080/21645698.2024.2376415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 07/01/2024] [Indexed: 07/11/2024]
Abstract
The ability to transfer information about the performance, safety, and environmental impacts of a genetically modified (GM) crop from confined field trials (CFTs) conducted in one location to another is increasingly gaining importance in biosafety regulatory assessment and decision-making. The CFT process can be expensive, time-consuming, and logistically challenging. Data transportability can help overcome these challenges by allowing the use of data obtained from CFTs conducted in one country to inform regulatory decision-making in another country. Applicability of transported CFT data would be particularly beneficial to the public sector product developers and small enterprises that develop innovative GM events but cannot afford to replicate redundant CFTs, as well as regulatory authorities seeking to improve the deployment of limited resources. This review investigates case studies where transported CFT data have successfully been applied in biosafety assessment and decision-making, with an outlook of how African countries could benefit from a similar approach.
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Affiliation(s)
- Paul Chege
- Program for Biosafety Systems (PBS), International Service for the Acquisition of Agri-biotech Applications (ISAAA AfriCenter), Nairobi, Kenya
- Program for Biosafety Systems (PBS), International Food Policy Institute (IFPRI), Washington, WA, USA
| | - Julia Njagi
- Inspection, National Biosafety Authority (NBA), Nairobi, Kenya
| | - John Komen
- Program for Biosafety Systems (PBS), International Food Policy Institute (IFPRI), Washington, WA, USA
| | - Godfrey Ngure
- Program for Biosafety Systems (PBS), International Service for the Acquisition of Agri-biotech Applications (ISAAA AfriCenter), Nairobi, Kenya
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Japan
| | - John Muriuki
- Environmental Science, Kenyatta University, Nairobi, Kenya
| | - Margaret Karembu
- Program for Biosafety Systems (PBS), International Service for the Acquisition of Agri-biotech Applications (ISAAA AfriCenter), Nairobi, Kenya
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26
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Miao L, Zhang J, Xu W, Qian Q, Zhang G, Yuan Q, Lv Y, Zhang H, Shen C, Wang W. Global research trends in CAR-T cell therapy for solid tumors: A comprehensive visualization and bibliometric study (2012-2023). Hum Vaccin Immunother 2024; 20:2338984. [PMID: 38698555 PMCID: PMC11073418 DOI: 10.1080/21645515.2024.2338984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/02/2024] [Indexed: 05/05/2024] Open
Abstract
CAR-T cell therapy has emerged as a significant approach for the management of hematological malignancies. Over the past few years, the utilization of CAR-T cells in the investigation and treatment of solid tumors has gained momentum, thereby establishing itself as a prominent area of research. This descriptive study involved the retrieval of articles about CAR-T cell therapy for solid tumors from the Web of Science Core Collection (WoSCC) database. Subsequently, bibliometric analysis and knowledge map analysis were conducted on these articles. The field under consideration is currently experiencing a period of swift advancement, as evidenced by the escalating number of publications in this domain each year. The United States holds an indisputable position as the foremost leader in this particular field, with the University of Pennsylvania emerging as the most active institution. The authors with the highest citation frequency and co-citation frequency are Carl H. June and Shannon L. Maude, respectively. The research hotspots in this field mainly focus on five aspects. Additionally, 10 emerging themes were identified. This study undertakes a comprehensive, systematic, and objective analysis and exploration of the field of CAR-T cell treatment for solid tumors, utilizing bibliometric methods. The findings of this study are expected to serve as a valuable reference and enlightenment for future research endeavors in this particular domain.
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Affiliation(s)
- Lele Miao
- Department of Thyroid and Breast Surgery, Jining NO.1 People’s Hospital, Jining, China
| | - Juan Zhang
- Department of Hematology, Jining NO.1 People’s Hospital, Jining, China
| | - Wei Xu
- Department of Thyroid and Breast Surgery, Jining NO.1 People’s Hospital, Jining, China
| | - Qian Qian
- Department of Thyroid and Breast Surgery, Jining NO.1 People’s Hospital, Jining, China
| | - Guochao Zhang
- Department of Thyroid and Breast Surgery, Jining NO.1 People’s Hospital, Jining, China
| | - Quan Yuan
- Department of Thyroid and Breast Surgery, Jining NO.1 People’s Hospital, Jining, China
| | - Yuetao Lv
- Department of Thyroid and Breast Surgery, Jining NO.1 People’s Hospital, Jining, China
| | - Haiguo Zhang
- Department of Hematology, Jining NO.1 People’s Hospital, Jining, China
| | - Chaoyan Shen
- Department of Ultrasound, Jining NO.1 People’s Hospital, Jining, China
| | - Wei Wang
- Department of Thyroid and Breast Surgery, Jining NO.1 People’s Hospital, Jining, China
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27
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Yao R, Xie C, Xia X. Recent progress in mRNA cancer vaccines. Hum Vaccin Immunother 2024; 20:2307187. [PMID: 38282471 PMCID: PMC10826636 DOI: 10.1080/21645515.2024.2307187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/16/2024] [Indexed: 01/30/2024] Open
Abstract
The research and development of messenger RNA (mRNA) cancer vaccines have gradually overcome numerous challenges through the application of personalized cancer antigens, structural optimization of mRNA, and the development of alternative RNA-based vectors and efficient targeted delivery vectors. Clinical trials are currently underway for various cancer vaccines that encode tumor-associated antigens (TAAs), tumor-specific antigens (TSAs), or immunomodulators. In this paper, we summarize the optimization of mRNA and the emergence of RNA-based expression vectors in cancer vaccines. We begin by reviewing the advancement and utilization of state-of-the-art targeted lipid nanoparticles (LNPs), followed by presenting the primary classifications and clinical applications of mRNA cancer vaccines. Collectively, mRNA vaccines are emerging as a central focus in cancer immunotherapy, offering the potential to address multiple challenges in cancer treatment, either as standalone therapies or in combination with current cancer treatments.
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Affiliation(s)
- Ruhui Yao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Chunyuan Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiaojun Xia
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
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28
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Qiaerxie G, Jiang Y, Li G, Yang Z, Long F, Yu Y, Lu JS, Du P, Cui Y. Design and evaluation of mRNA encoding recombinant neutralizing antibodies for botulinum neurotoxin type B intoxication prophylaxis. Hum Vaccin Immunother 2024; 20:2358570. [PMID: 38853516 PMCID: PMC11168212 DOI: 10.1080/21645515.2024.2358570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/18/2024] [Indexed: 06/11/2024] Open
Abstract
Among all natural and synthetic toxins, botulinum neurotoxins (BoNTs), produced by Clostridium botulinum in an anaerobic environment, are the most toxic polymer proteins. Currently, the most effective modalities for botulism prevention and treatment are vaccination and antitoxin use, respectively. However, these modalities are associated with long response time for active immunization, side effects, and donor limitations. As such, the development of more promising botulism prevention and treatment modalities is warranted. Here, we designed an mRNA encoding B9-hFc - a heavy-chain antibody fused to VHH and human Fc that can neutralize BoNT serotype B (BoNT/B) effectively - and assessed its expression in vitro and in vivo. The results confirmed that our mRNA demonstrates good expression in vitro and in vivo. Moreover, a single mRNA lipid nanoparticle injection effectively prevents BoNT/B intoxication in vivo, with effects comparable to those of protein antibodies. In conclusion, we explored and clarified whether mRNA drugs encoding neutralizing antibodies prevent BoNT/B intoxication. Our results provide an efficient strategy for further research on the prevention and treatment of intoxication by botulinum toxin.
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Affiliation(s)
- Gulisaina Qiaerxie
- School of Medical Device, Shenyang Pharmaceutical University, Shenyang, Liaoning, China
- Protein Engineering Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Yujia Jiang
- Protein Engineering Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Gege Li
- School of Medical Device, Shenyang Pharmaceutical University, Shenyang, Liaoning, China
- Protein Engineering Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Zhixin Yang
- Protein Engineering Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Feng Long
- School of Medical Device, Shenyang Pharmaceutical University, Shenyang, Liaoning, China
- Department of Pharmacy, Maternal and Child Health Care Hospital of Zaozhuang, Zaozhuang, Shandong, China
| | - Yunzhou Yu
- Protein Engineering Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Jian Sheng Lu
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing, China
| | - Peng Du
- Protein Engineering Laboratory, Beijing Institute of Biotechnology, Beijing, China
| | - Yong Cui
- School of Medical Device, Shenyang Pharmaceutical University, Shenyang, Liaoning, China
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29
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Grieve LM, Rani A, ZeRuth GT. Downregulation of Glis3 in INS1 cells exposed to chronically elevated glucose contributes to glucotoxicity-associated β cell dysfunction. Islets 2024; 16:2344622. [PMID: 38652652 PMCID: PMC11042057 DOI: 10.1080/19382014.2024.2344622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/15/2024] [Indexed: 04/25/2024] Open
Abstract
Chronically elevated levels of glucose are deleterious to pancreatic β cells and contribute to β cell dysfunction, which is characterized by decreased insulin production and a loss of β cell identity. The Krüppel-like transcription factor, Glis3 has previously been shown to positively regulate insulin transcription and mutations within the Glis3 locus have been associated with the development of several pathologies including type 2 diabetes mellitus. In this report, we show that Glis3 is significantly downregulated at the transcriptional level in INS1 832/13 cells within hours of being subjected to high glucose concentrations and that diminished expression of Glis3 is at least partly attributable to increased oxidative stress. CRISPR/Cas9-mediated knockdown of Glis3 indicated that the transcription factor was required to maintain normal levels of both insulin and MafA expression and reduced Glis3 expression was concomitant with an upregulation of β cell disallowed genes. We provide evidence that Glis3 acts similarly to a pioneer factor at the insulin promoter where it permissively remodels the chromatin to allow access to a transcriptional regulatory complex including Pdx1 and MafA. Finally, evidence is presented that Glis3 can positively regulate MafA transcription through its pancreas-specific promoter and that MafA reciprocally regulates Glis3 expression. Collectively, these results suggest that decreased Glis3 expression in β cells exposed to chronic hyperglycemia may contribute significantly to reduced insulin transcription and a loss of β cell identity.
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Affiliation(s)
- LilyAnne M. Grieve
- Department of Biological Sciences, Murray State University, Murray, KY, USA
| | - Abhya Rani
- Department of Biological Sciences, Murray State University, Murray, KY, USA
| | - Gary T. ZeRuth
- Department of Biological Sciences, Murray State University, Murray, KY, USA
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30
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Yang S, Wang G, Niu M, Zhang H, Ma J, Qu C, Liu G. Impacts of AlaAT3 transgenic poplar on rhizosphere soil chemical properties, enzyme activity, bacterial community, and metabolites under two nitrogen conditions. GM CROPS & FOOD 2024; 15:1-15. [PMID: 38625676 PMCID: PMC11028027 DOI: 10.1080/21645698.2024.2339568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/02/2024] [Indexed: 04/17/2024]
Abstract
Poplar stands as one of the primary afforestation trees globally. We successfully generated transgenic poplar trees characterized by enhanced biomass under identical nutrient conditions, through the overexpression of the pivotal nitrogen assimilation gene, pxAlaAT3. An environmental risk assessment was conducted for investigate the potential changes in rhizosphere soil associated with these overexpressing lines (OL). The results show that acid phosphatase activity was significantly altered under ammonium in OL compared to the wild-type control (WT), and a similar difference was observed for protease under nitrate. 16SrDNA sequencing indicated no significant divergence in rhizosphere soil microbial community diversity between WT and OL. Metabolomics analysis revealed that the OL caused minimal alterations in the metabolites of the rhizosphere soil, posing no potential harm to the environment. With these findings in mind, we anticipate that overexpressed plants will not adversely impact the surrounding soil environment.
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Affiliation(s)
| | - Gang Wang
- Guizhou Institute of Walnut, Guizhou Academy of Forestry, Guiyang, China
| | - Minghui Niu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Heng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Jing Ma
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Chunpu Qu
- College of Foresty, Guizhou University, Guiyang, China
| | - Guanjun Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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31
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Sangprasat K, Bulaon CJI, Rattanapisit K, Srisangsung T, Jirarojwattana P, Wongwatanasin A, Phoolcharoen W. Production of monoclonal antibodies against botulinum neurotoxin in Nicotiana benthamiana. Hum Vaccin Immunother 2024; 20:2329446. [PMID: 38525945 DOI: 10.1080/21645515.2024.2329446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/08/2024] [Indexed: 03/26/2024] Open
Abstract
Botulism is a fatal neurologic disease caused by the botulinum toxin (BoNT) produced by Clostridium botulinum. It is a rare but highly toxic disease with symptoms, such as cramps, nausea, vomiting, diarrhea, dysphagia, respiratory failure, muscle weakness, and even death. Currently, two types of antitoxin are used: equine-derived heptavalent antitoxin and human-derived immunoglobulin (BabyBIG®). However, heptavalent treatment may result in hypersensitivity, whereas BabyBIG®, has a low yield. The present study focused on the development of three anti-BoNT monoclonal antibodies (mAbs), 1B18, C25, and M2, in Nicotiana benthamiana. The plant-expressed mAbs were purified and examined for size, purity and integrity by SDS-PAGE, western blotting and size-exclusion chromatography. Analysis showed that plant-produced anti-BoNT mAbs can fully assemble in plants, can be purified in a single purification step, and mostly remain as monomeric proteins. The efficiency of anti-BoNT mAbs binding to BoNT/A and B was then tested. Plant-produced 1B18 retained its ability to recognize both mBoNT/A1 and ciBoNT/B1. At the same time, the binding specificities of two other mAbs were determined: C25 for mBoNT/A1 and M2 for ciBoNT/B1. In conclusion, our results confirm the use of plants as an alternative platform for the production of anti-BoNT mAbs. This plant-based technology will serve as a versatile system for the development botulism immunotherapeutics.
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Affiliation(s)
- Kornchanok Sangprasat
- Center of Excellence in Plant-Produced Pharmaceuticals, Chulalongkorn University, Bangkok, Thailand
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
- Graduate Program of Program in Research for Enterprise, Chulalongkorn University, Bangkok, Thailand
| | | | - Kaewta Rattanapisit
- Department of Research and Development, Baiya Phytopharm Co. Ltd, Bangkok, Thailand
| | - Theerakarn Srisangsung
- Center of Excellence in Plant-Produced Pharmaceuticals, Chulalongkorn University, Bangkok, Thailand
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
- Graduate Program of Program in Research for Enterprise, Chulalongkorn University, Bangkok, Thailand
| | - Perawat Jirarojwattana
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | | | - Waranyoo Phoolcharoen
- Center of Excellence in Plant-Produced Pharmaceuticals, Chulalongkorn University, Bangkok, Thailand
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
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Hu H, Wei XY, Liu L, Wang YB, Bu LK, Jia HJ, Pei DS. Biogeographic patterns of meio- and micro-eukaryotic communities in dam-induced river-reservoir systems. Appl Microbiol Biotechnol 2024; 108:130. [PMID: 38229334 DOI: 10.1007/s00253-023-12993-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 10/30/2023] [Accepted: 12/28/2023] [Indexed: 01/18/2024]
Abstract
Although the Three Gorges Dam (TGD) is the world's largest hydroelectric dam, little is known about the spatial-temporal patterns and community assembly mechanisms of meio- and micro-eukaryotes and its two subtaxa (zooplankton and zoobenthos). This knowledge gap is particularly evident across various habitats and during different water-level periods, primarily arising from the annual regular dam regulation. To address this inquiry, we employed mitochondrial cytochrome c oxidase I (COI) gene-based environmental DNA (eDNA) metabarcoding technology to systematically analyze the biogeographic pattern of the three communities within the Three Gorges Reservoir (TGR). Our findings reveal distinct spatiotemporal characteristics and complementary patterns in the distribution of meio- and micro-eukaryotes. The three communities showed similar biogeographic patterns and assembly processes. Notably, the diversity of these three taxa gradually decreased along the river. Their communities were less shaped by stochastic processes, which gradually decreased along the longitudinal riverine-transition-lacustrine gradient. Hence, deterministic factors, such as seasonality, environmental, and spatial variables, along with species interactions, likely play a pivotal role in shaping these communities. Environmental factors primarily drive seasonal variations in these communities, while hydrological conditions, represented as spatial distance, predominantly influence spatial variations. These three communities followed the distance-decay pattern. In winter, compared to summer, both the decay and species interrelationships are more pronounced. Taken together, this study offers fresh insights into the composition and diversity patterns of meio- and micro-eukaryotes at the spatial-temporal level. It also uncovers the mechanisms behind community assembly in various environmental niches within the dam-induced river-reservoir systems. KEY POINTS: • Distribution and diversity of meio- and micro-eukaryotes exhibit distinct spatiotemporal patterns in the TGR. • Contribution of stochastic processes in community assembly gradually decreases along the river. • Deterministic factors and species interactions shape meio- and micro-eukaryotic community.
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Affiliation(s)
- Huan Hu
- Chongqing Jiaotong University, Chongqing, 400074, China
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Xing-Yi Wei
- Chongqing Jiaotong University, Chongqing, 400074, China
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Li Liu
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Yuan-Bo Wang
- Chongqing Jiaotong University, Chongqing, 400074, China
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Ling-Kang Bu
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China
| | - Huang-Jie Jia
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - De-Sheng Pei
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China.
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Qiao Y, Yang R, Liu Y, Chen J, Zhao L, Huo P, Wang Z, Bu D, Wu Y, Zhao Y. DeepFusion: A deep bimodal information fusion network for unraveling protein-RNA interactions using in vivo RNA structures. Comput Struct Biotechnol J 2024; 23:617-625. [PMID: 38274994 PMCID: PMC10808905 DOI: 10.1016/j.csbj.2023.12.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/04/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
RNA-binding proteins (RBPs) are key post-transcriptional regulators, and the malfunctions of RBP-RNA binding lead to diverse human diseases. However, prediction of RBP binding sites is largely based on RNA sequence features, whereas in vivo RNA structural features based on high-throughput sequencing are rarely incorporated. Here, we designed a deep bimodal information fusion network called DeepFusion for unraveling protein-RNA interactions by incorporating structural features derived from DMS-seq data. DeepFusion integrates two sub-models to extract local motif-like information and long-term context information. We show that DeepFusion performs best compared with other cutting-edge methods with only sequence inputs on two datasets. DeepFusion's performance is further improved with bimodal input after adding in vivo DMS-seq structural features. Furthermore, DeepFusion can be used for analyzing RNA degradation, demonstrating significantly different RBP-binding scores in genes with slow degradation rates versus those with rapid degradation rates. DeepFusion thus provides enhanced abilities for further analysis of functional RNAs. DeepFusion's code and data are available at http://bioinfo.org/deepfusion/.
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Affiliation(s)
- Yixuan Qiao
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Yang
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Liu
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaxin Chen
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Lianhe Zhao
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Peipei Huo
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhihao Wang
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Dechao Bu
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Yang Wu
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Yi Zhao
- Research Center for Ubiquitous Computing Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Liu X, Wang H, Gao J. scIALM: A method for sparse scRNA-seq expression matrix imputation using the Inexact Augmented Lagrange Multiplier with low error. Comput Struct Biotechnol J 2024; 23:549-558. [PMID: 38274995 PMCID: PMC10809077 DOI: 10.1016/j.csbj.2023.12.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/27/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is a high-throughput sequencing technology that quantifies gene expression profiles of specific cell populations at the single-cell level, providing a foundation for studying cellular heterogeneity and patient pathological characteristics. It is effective for developmental, fertility, and disease studies. However, the cell-gene expression matrix of single-cell sequencing data is often sparse and contains numerous zero values. Some of the zero values derive from noise, where dropout noise has a large impact on downstream analysis. In this paper, we propose a method named scIALM for imputation recovery of sparse single-cell RNA data expression matrices, which employs the Inexact Augmented Lagrange Multiplier method to use sparse but clean (accurate) data to recover unknown entries in the matrix. We perform experimental analysis on four datasets, calling the expression matrix after Quality Control (QC) as the original matrix, and comparing the performance of scIALM with six other methods using mean squared error (MSE), mean absolute error (MAE), Pearson correlation coefficient (PCC), and cosine similarity (CS). Our results demonstrate that scIALM accurately recovers the original data of the matrix with an error of 10e-4, and the mean value of the four metrics reaches 4.5072 (MSE), 0.765 (MAE), 0.8701 (PCC), 0.8896 (CS). In addition, at 10%-50% random masking noise, scIALM is the least sensitive to the masking ratio. For downstream analysis, this study uses adjusted rand index (ARI) and normalized mutual information (NMI) to evaluate the clustering effect, and the results are improved on three datasets containing real cluster labels.
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Affiliation(s)
- Xiaohong Liu
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Han Wang
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jingyang Gao
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
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Yan Q, Zhang Y, Hou R, Pan W, Liang H, Gao X, Deng W, Huang X, Qu L, Tang C, He P, Liu B, Wang Q, Zhao X, Lin Z, Chen Z, Li P, Han J, Xiong X, Zhao J, Li S, Niu X, Chen L. Deep immunoglobulin repertoire sequencing depicts a comprehensive atlas of spike-specific antibody lineages shared among COVID-19 convalescents. Emerg Microbes Infect 2024; 13:2290841. [PMID: 38044868 PMCID: PMC10810631 DOI: 10.1080/22221751.2023.2290841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
Neutralizing antibodies are a key component in protective humoral immunity against SARS-CoV-2. Currently, available technologies cannot track epitope-specific antibodies in global antibody repertoires. Thus, the comprehensive repertoire of spike-specific neutralizing antibodies elicited by SARS-CoV-2 infection is not fully understood. We therefore combined high-throughput immunoglobulin heavy chain (IgH) repertoire sequencing, and structural and bioinformatics analysis to establish an antibodyomics pipeline, which enables tracking spike-specific antibody lineages that target certain neutralizing epitopes. We mapped the neutralizing epitopes on the spike and determined the epitope-preferential antibody lineages. This analysis also revealed numerous overlaps between immunodominant neutralizing antibody-binding sites and mutation hotspots on spikes as observed so far in SARS-CoV-2 variants. By clustering 2677 spike-specific antibodies with 360 million IgH sequences that we sequenced, a total of 329 shared spike-specific antibody clonotypes were identified from 33 COVID-19 convalescents and 24 SARS-CoV-2-naïve individuals. Epitope mapping showed that the shared antibody responses target not only neutralizing epitopes on RBD and NTD but also non-neutralizing epitopes on S2. The immunodominance of neutralizing antibody response is determined by the occurrence of specific precursors in human naïve B-cell repertoires. We identified that only 28 out of the 329 shared spike-specific antibody clonotypes persisted for at least 12 months. Among them, long-lived IGHV3-53 antibodies are likely to evolve cross-reactivity to Omicron variants through accumulating somatic hypermutations. Altogether, we created a comprehensive atlas of spike-targeting antibody lineages in COVID-19 convalescents and antibody precursors in human naïve B cell repertoires, providing a valuable reference for future vaccine design and evaluation.
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Affiliation(s)
- Qihong Yan
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Yudi Zhang
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- University of Chinese Academy of Science, Beijing, People’s Republic of China
| | - Ruitian Hou
- Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Wenjing Pan
- Hengyang Medical School, University of South China, Hengyang, People’s Republic of China
- Nanjing ARP Biotechnology Co., Ltd, Nanjing, People’s Republic of China
| | - Huan Liang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Xijie Gao
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Weiqi Deng
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- University of Chinese Academy of Science, Beijing, People’s Republic of China
| | - Xiaohan Huang
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Linbing Qu
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Congli Tang
- Nanjing ARP Biotechnology Co., Ltd, Nanjing, People’s Republic of China
| | - Ping He
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Banghui Liu
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Qian Wang
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Xinwei Zhao
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Zihan Lin
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- University of Chinese Academy of Science, Beijing, People’s Republic of China
| | - Zhaoming Chen
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Pingchao Li
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Jian Han
- iRepertoire Inc., Huntsville, AL, USA
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Song Li
- Hengyang Medical School, University of South China, Hengyang, People’s Republic of China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
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Yao M, Zhang L, Teng X, Lei Y, Xing X, Ren T, Pan Y, Zhang L, Li Z, Lin J, Zheng Y, Xing L, Zhou J, Wu C. Transcriptomic profiling of Dip2a in the neural differentiation of mouse embryonic stem cells. Comput Struct Biotechnol J 2024; 23:700-710. [PMID: 38292475 PMCID: PMC10825174 DOI: 10.1016/j.csbj.2023.12.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 02/01/2024] Open
Abstract
Introduction The disconnected-interacting protein 2 homolog A (DIP2A), a member of disconnected-interacting 2 protein family, has been shown to be involved in human nervous system-related mental illness. This protein is highly expressed in the nervous system of mouse. Mutation of mouse DIP2A causes defects in spine morphology and synaptic transmission, autism-like behaviors, and defective social novelty [5], [27], indicating that DIP2A is critical to the maintenance of neural development. However, the role of DIP2A in neural differentiation has yet to be investigated. Objective To determine the role of DIP2A in neural differentiation, a neural differentiation model was established using mouse embryonic stem cells (mESCs) and studied by using gene-knockout technology and RNA-sequencing-based transcriptome analysis. Results We found that DIP2A is not required for mESCs pluripotency maintenance, but loss of DIP2A causes the neural differentiation abnormalities in both N2B27 and KSR medium. Functional knockout of Dip2a gene also decreased proliferation of mESCs by perturbation of the cell cycle and profoundly inhibited the expression of a large number of neural development-associated genes which mainly enriched in spinal cord development and postsynapse assembly. Conclusions The results of this report demonstrate that DIP2A plays an essential role in regulating differentiation of mESCs towards the neural fate.
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Affiliation(s)
- Mingze Yao
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Lei Zhang
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
- Center of Reproductive Medicine, Children's Hospital of Shanxi and Women Health Center of Shanxi, Taiyuan 030006, China
| | - Xiaojuan Teng
- Dermatology Hospital, Southern Medical University, Guangzhou 510000, China
| | - Yu Lei
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Xiaoyu Xing
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Tinglin Ren
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Yuanqing Pan
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Liwen Zhang
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Zhengfeng Li
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510000, China
| | - Jingxia Lin
- Dermatology Hospital, Southern Medical University, Guangzhou 510000, China
| | - Yaowu Zheng
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Li Xing
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Jiajian Zhou
- Dermatology Hospital, Southern Medical University, Guangzhou 510000, China
| | - Changxin Wu
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
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Rosati D, Palmieri M, Brunelli G, Morrione A, Iannelli F, Frullanti E, Giordano A. Differential gene expression analysis pipelines and bioinformatic tools for the identification of specific biomarkers: A review. Comput Struct Biotechnol J 2024; 23:1154-1168. [PMID: 38510977 PMCID: PMC10951429 DOI: 10.1016/j.csbj.2024.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
In recent years, the role of bioinformatics and computational biology together with omics techniques and transcriptomics has gained tremendous importance in biomedicine and healthcare, particularly for the identification of biomarkers for precision medicine and drug discovery. Differential gene expression (DGE) analysis is one of the most used techniques for RNA-sequencing (RNA-seq) data analysis. This tool, which is typically used in various RNA-seq data processing applications, allows the identification of differentially expressed genes across two or more sample sets. Functional enrichment analyses can then be performed to annotate and contextualize the resulting gene lists. These studies provide valuable information about disease-causing biological processes and can help in identifying molecular targets for novel therapies. This review focuses on differential gene expression (DGE) analysis pipelines and bioinformatic techniques commonly used to identify specific biomarkers and discuss the advantages and disadvantages of these techniques.
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Affiliation(s)
- Diletta Rosati
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Cancer Genomics & Systems Biology Lab, Dept. of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy
| | - Maria Palmieri
- Cancer Genomics & Systems Biology Lab, Dept. of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy
| | - Giulia Brunelli
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy
| | - Andrea Morrione
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Francesco Iannelli
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Elisa Frullanti
- Cancer Genomics & Systems Biology Lab, Dept. of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy
| | - Antonio Giordano
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
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Lu X, Xie L, Xu L, Mao R, Xu X, Chang S. Multimodal fused deep learning for drug property prediction: Integrating chemical language and molecular graph. Comput Struct Biotechnol J 2024; 23:1666-1679. [PMID: 38680871 PMCID: PMC11046066 DOI: 10.1016/j.csbj.2024.04.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/01/2024] [Accepted: 04/10/2024] [Indexed: 05/01/2024] Open
Abstract
Accurately predicting molecular properties is a challenging but essential task in drug discovery. Recently, many mono-modal deep learning methods have been successfully applied to molecular property prediction. However, mono-modal learning is inherently limited as it relies solely on a single modality of molecular representation, which restricts a comprehensive understanding of drug molecules. To overcome the limitations, we propose a multimodal fused deep learning (MMFDL) model to leverage information from different molecular representations. Specifically, we construct a triple-modal learning model by employing Transformer-Encoder, Bidirectional Gated Recurrent Unit (BiGRU), and graph convolutional network (GCN) to process three modalities of information from chemical language and molecular graph: SMILES-encoded vectors, ECFP fingerprints, and molecular graphs, respectively. We evaluate the proposed triple-modal model using five fusion approaches on six molecule datasets, including Delaney, Llinas2020, Lipophilicity, SAMPL, BACE, and pKa from DataWarrior. The results show that the MMFDL model achieves the highest Pearson coefficients, and stable distribution of Pearson coefficients in the random splitting test, outperforming mono-modal models in accuracy and reliability. Furthermore, we validate the generalization ability of our model in the prediction of binding constants for protein-ligand complex molecules, and assess the resilience capability against noise. Through analysis of feature distributions in chemical space and the assigned contribution of each modal model, we demonstrate that the MMFDL model shows the ability to acquire complementary information by using proper models and suitable fusion approaches. By leveraging diverse sources of bioinformatics information, multimodal deep learning models hold the potential for successful drug discovery.
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Affiliation(s)
- Xiaohua Lu
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Liangxu Xie
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Rongzhi Mao
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Xiaojun Xu
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China
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Mizoguchi T. In vivo dynamics of hard tissue-forming cell origins: Insights from Cre/loxP-based cell lineage tracing studies. JAPANESE DENTAL SCIENCE REVIEW 2024; 60:109-119. [PMID: 38406212 PMCID: PMC10885318 DOI: 10.1016/j.jdsr.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/27/2024] Open
Abstract
Bone tissue provides structural support for our bodies, with the inner bone marrow (BM) acting as a hematopoietic organ. Within the BM tissue, two types of stem cells play crucial roles: mesenchymal stem cells (MSCs) (or skeletal stem cells) and hematopoietic stem cells (HSCs). These stem cells are intricately connected, where BM-MSCs give rise to bone-forming osteoblasts and serve as essential components in the BM microenvironment for sustaining HSCs. Despite the mid-20th century proposal of BM-MSCs, their in vivo identification remained elusive owing to a lack of tools for analyzing stemness, specifically self-renewal and multipotency. To address this challenge, Cre/loxP-based cell lineage tracing analyses are being employed. This technology facilitated the in vivo labeling of specific cells, enabling the tracking of their lineage, determining their stemness, and providing a deeper understanding of the in vivo dynamics governing stem cell populations responsible for maintaining hard tissues. This review delves into cell lineage tracing studies conducted using commonly employed genetically modified mice expressing Cre under the influence of LepR, Gli1, and Axin2 genes. These studies focus on research fields spanning long bones and oral/maxillofacial hard tissues, offering insights into the in vivo dynamics of stem cell populations crucial for hard tissue homeostasis.
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Zeng W, Zheng L, Li Y, Yang J, Mao T, Zhang J, Liu Y, Ning J, Zhang T, Huang H, Chen X, Lu F. Engineered extracellular vesicles for delivering functional Cas9/gRNA to eliminate hepatitis B virus cccDNA and integration. Emerg Microbes Infect 2024; 13:2284286. [PMID: 37982370 PMCID: PMC10763861 DOI: 10.1080/22221751.2023.2284286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 11/13/2023] [Indexed: 11/21/2023]
Abstract
The persistence of HBV covalently closed circular DNA (cccDNA) and HBV integration into the host genome in infected hepatocytes pose significant challenges to the cure of chronic HBV infection. Although CRISPR/Cas9-mediated genome editing shows promise for targeted clearance of viral genomes, a safe and efficient delivery method is currently lacking. Here, we developed a novel approach by combining light-induced heterodimerization and protein acylation to enhance the loading efficiency of Cas9 protein into extracellular vesicles (EVs). Moreover, vesicular stomatitis virus-glycoprotein (VSV-G) was incorporated onto the EVs membrane, significantly facilitating the endosomal escape of Cas9 protein and increasing its gene editing activity in recipient cells. Our results demonstrated that engineered EVs containing Cas9/gRNA and VSV-G can effectively reduce viral antigens and cccDNA levels in the HBV-replicating and infected cell models. Notably, we also confirmed the antiviral activity and high safety of the engineered EVs in the HBV-replicating mouse model generated by hydrodynamic injection and the HBV transgenic mouse model. In conclusion, engineered EVs could successfully mediate functional CRISPR/Cas9 delivery both in vitro and in vivo, leading to the clearance of episomal cccDNA and integrated viral DNA fragments, and providing a novel therapeutic approach for curing chronic HBV infection.
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Affiliation(s)
- Wanjia Zeng
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People’s Republic of China
| | - Liwei Zheng
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People’s Republic of China
| | - Yukun Li
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People’s Republic of China
| | - Jing Yang
- School of Medicine, Shihezi University, Shihezi, People’s Republic of China
| | - Tianhao Mao
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People’s Republic of China
| | - Jing Zhang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People’s Republic of China
| | - Yanna Liu
- Department of Gastroenterology and Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Jing Ning
- Department of Gastroenterology, Beijing Key Laboratory for Helicobacter Pylori Infection and Upper Gastrointestinal Diseases, Peking University Third Hospital, Beijing, People’s Republic of China
| | - Ting Zhang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People’s Republic of China
| | - Hongxin Huang
- Department of Pathogen Biology and Biosecurity, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Xiangmei Chen
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People’s Republic of China
| | - Fengmin Lu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People’s Republic of China
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Ahmed NM, Mohamed MS, Awad SM, Abd El-Hameed RH, El-tawab NAA, Gaballah MS, Said AM. Design, synthesis, molecular modelling and biological evaluation of novel 6-amino-5-cyano-2-thiopyrimidine derivatives as potent anticancer agents against leukemia and apoptotic inducers. J Enzyme Inhib Med Chem 2024; 39:2304625. [PMID: 38348824 PMCID: PMC10866072 DOI: 10.1080/14756366.2024.2304625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 01/08/2024] [Indexed: 02/15/2024] Open
Abstract
Herein, a novel series of 6-amino-5-cyano-2-thiopyrimidines and condensed pyrimidines analogues were prepared. All the synthesized compounds (1a-c, 2a-c, 3a-c, 4a-r and 5a-c) were evaluated for in vitro anticancer activity by the National Cancer Institute (NCI; MD, USA) against 60 cell lines. Compound 1c showed promising anticancer activity and was selected for the five-dose testing. Results demonstrated that compound 1c possessed broad spectrum anti-cancer activity against the nine cancerous subpanels tested with selectivity ratio ranging from 0.7 to 39 at the GI50 level with high selectivity towards leukaemia. Mechanistic studies showed that Compound 1c showed comparable activity to Duvelisib against PI3Kδ (IC50 = 0.0034 and 0.0025 μM, respectively) and arrested cell cycle at the S phase and displayed significant increase in the early and late apoptosis in HL60 and leukaemia SR cells. The necrosis percentage showed a significant increase from 1.13% to 3.41% in compound 1c treated HL60 cells as well as from 1.51% to 4.72% in compound 1c treated leukaemia SR cells. Also, compound 1c triggered apoptosis by activating caspase 3, Bax, P53 and suppressing Bcl2. Moreover, 1c revealed a good safety profile against human normal lung fibroblast cell line (WI-38 cells). Molecular analysis of Duvelisib and compound 1c in PI3K was performed. Finally, these results suggest that 2-thiopyrimidine derivative 1c might serve as a model for designing novel anticancer drugs in the future.
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Affiliation(s)
- Naglaa M. Ahmed
- Pharmaceutical Organic Chemistry Department, Helwan University, Ein-Helwan, Egypt
| | - Mosaad S. Mohamed
- Pharmaceutical Organic Chemistry Department, Helwan University, Ein-Helwan, Egypt
| | - Samir M. Awad
- Pharmaceutical Organic Chemistry Department, Helwan University, Ein-Helwan, Egypt
| | | | | | - Mohamed S. Gaballah
- Biochemistry and Molecular Biology Department, Helwan University, Ein-Helwan, Egypt
| | - Ahmed M. Said
- Pharmaceutical Organic Chemistry Department, Helwan University, Ein-Helwan, Egypt
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, USA
- Athenex Inc, Buffalo, NY, USA
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Oh KK, Yoon SJ, Song SH, Park JH, Kim JS, Kim DJ, Suk KT. The synchronized feature of Saururus chinensis and gut microbiota against T2DM, NAFLD, obesity and hypertension via integrated pharmacology. ARTIFICIAL CELLS, NANOMEDICINE, AND BIOTECHNOLOGY 2024; 52:278-290. [PMID: 38733373 DOI: 10.1080/21691401.2024.2350475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024]
Abstract
Type 2 diabetes mellitus (T2DM), nonalcoholic fatty liver disease (NAFLD), obesity (OB) and hypertension (HT) are categorized as metabolic disorders (MDs), which develop independently without distinct borders. Herein, we examined the gut microbiota (GM) and Saururus chinensis (SC) to confirm their therapeutic effects via integrated pharmacology. The overlapping targets from the four diseases were determined to be key protein coding genes. The protein-protein interaction (PPI) networks, and the SC, GM, signalling pathway, target and metabolite (SGSTM) networks were analysed via RPackage. Additionally, molecular docking tests (MDTs) and density functional theory (DFT) analysis were conducted to determine the affinity and stability of the conformer(s). TNF was the main target in the PPI analysis, and equol derived from Lactobacillus paracasei JS1 was the most effective agent for the formation of the TNF complex. The SC agonism (PPAR signalling pathway), and antagonism (neurotrophin signalling pathway) by SC were identified as agonistic bioactives (aromadendrane, stigmasta-5,22-dien-3-ol, 3,6,6-trimethyl-3,4,5,7,8,9-hexahydro-1H-2-benzoxepine, 4α-5α-epoxycholestane and kinic acid), and antagonistic bioactives (STK734327 and piclamilast), respectively, via MDT. Finally, STK734327-MAPK1 was the most favourable conformer according to DFT. Overall, the seven bioactives from SC and equol that can be produced by Lactobacillus paracasei JS1 can exert synergistic effects on these four diseases.
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Affiliation(s)
- Ki-Kwang Oh
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Sang-Jun Yoon
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Seol Hee Song
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Jeong Ha Park
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Jeong Su Kim
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Dong Joon Kim
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Ki-Tae Suk
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon, South Korea
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43
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Xia W, Shi N, Li C, Tang A. RNA-Seq and miRNA-Seq data from Epstein-Barr virus-infected tree shrews reveal a ceRNA network contributing to immune microenvironment regulation. Virulence 2024; 15:2306795. [PMID: 38251668 PMCID: PMC10826628 DOI: 10.1080/21505594.2024.2306795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
Epstein-Barr virus (EBV) infection in humans is ubiquitous and associated with various diseases. Remodeling of the immune microenvironment is the primary cause of EBV infection and pathogenesis; however, the underlying mechanism has not been fully elucidated. In this study, we used whole-transcriptome RNA-Seq to detect mRNAs, long non-coding RNAs (lncRNA), and microRNA (miRNA) profiles in the control group, 3 days, and 28 days after EBV infection, based on the tree shrew model that we reported previously. First, we estimated the proportion of 22 cell types in each sample using CIBERSORT software and identified 18 high-confidence DElncRNAs related to immune microenvironment regulation after EBV infection. Functional enrichment analysis of these differentially expressed lncRNAs primarily focused on the autophagy, endocytosis, and ferroptosis signalling pathways. Moreover, EBV infection affects miRNA expression patterns, and many miRNAs are silenced. Finally, three competing endogenous RNA regulatory networks were built using lncRNAs that significantly correlated with immune cell types, miRNAs that responded to EBV infection, and potentially targeted the mRNA of the miRNAs. Among them, MRPL42-AS-5 might act as an hsa-miR-296-5p "sponge" and compete with target mRNAs, thus increasing mRNA expression level, which could induce immune cell infiltration through the cellular senescence signalling pathway against EBV infection. Overall, we conducted a complete transcriptomic analysis of EBV infection in vivo for the first time and provided a novel perspective for further investigation of EBV-host interactions.
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Affiliation(s)
- Wei Xia
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Nanning, Guangxi, China
| | - Nan Shi
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Nanning, Guangxi, China
| | - Chaoqian Li
- Department of Emergency, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Anzhou Tang
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Ministry of Education, Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Nanning, Guangxi, China
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Kirk NM, Liang Y, Ly H. Pathogenesis and virulence of coronavirus disease: Comparative pathology of animal models for COVID-19. Virulence 2024; 15:2316438. [PMID: 38362881 PMCID: PMC10878030 DOI: 10.1080/21505594.2024.2316438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/04/2024] [Indexed: 02/17/2024] Open
Abstract
Animal models that can replicate clinical and pathologic features of severe human coronavirus infections have been instrumental in the development of novel vaccines and therapeutics. The goal of this review is to summarize our current understanding of the pathogenesis of coronavirus disease 2019 (COVID-19) and the pathologic features that can be observed in several currently available animal models. Knowledge gained from studying these animal models of SARS-CoV-2 infection can help inform appropriate model selection for disease modelling as well as for vaccine and therapeutic developments.
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Affiliation(s)
- Natalie M. Kirk
- Department of Veterinary & Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Twin Cities, MN, USA
| | - Yuying Liang
- Department of Veterinary & Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Twin Cities, MN, USA
| | - Hinh Ly
- Department of Veterinary & Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Twin Cities, MN, USA
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45
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Moeckel C, Mareboina M, Konnaris MA, Chan CS, Mouratidis I, Montgomery A, Chantzi N, Pavlopoulos GA, Georgakopoulos-Soares I. A survey of k-mer methods and applications in bioinformatics. Comput Struct Biotechnol J 2024; 23:2289-2303. [PMID: 38840832 PMCID: PMC11152613 DOI: 10.1016/j.csbj.2024.05.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 06/07/2024] Open
Abstract
The rapid progression of genomics and proteomics has been driven by the advent of advanced sequencing technologies, large, diverse, and readily available omics datasets, and the evolution of computational data processing capabilities. The vast amount of data generated by these advancements necessitates efficient algorithms to extract meaningful information. K-mers serve as a valuable tool when working with large sequencing datasets, offering several advantages in computational speed and memory efficiency and carrying the potential for intrinsic biological functionality. This review provides an overview of the methods, applications, and significance of k-mers in genomic and proteomic data analyses, as well as the utility of absent sequences, including nullomers and nullpeptides, in disease detection, vaccine development, therapeutics, and forensic science. Therefore, the review highlights the pivotal role of k-mers in addressing current genomic and proteomic problems and underscores their potential for future breakthroughs in research.
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Affiliation(s)
- Camille Moeckel
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Manvita Mareboina
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Maxwell A. Konnaris
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Candace S.Y. Chan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Ioannis Mouratidis
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Huck Institute of the Life Sciences, Penn State University, University Park, Pennsylvania, USA
| | - Austin Montgomery
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Nikol Chantzi
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | | | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Huck Institute of the Life Sciences, Penn State University, University Park, Pennsylvania, USA
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46
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Sardag I, Duvenci ZS, Belkaya S, Timucin E. Rational design of monomeric IL37 variants guided by stability and dynamical analyses of IL37 dimers. Comput Struct Biotechnol J 2024; 23:1854-1863. [PMID: 38882680 PMCID: PMC11177541 DOI: 10.1016/j.csbj.2024.04.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/07/2024] [Accepted: 04/14/2024] [Indexed: 06/18/2024] Open
Abstract
IL37 plays important roles in the regulation of innate immunity and its oligomeric status is critical to these roles. In its monomeric state, IL37 can effectively inhibit the inflammatory response of IL18 by binding to IL18Rα, a capacity lost in its dimeric form, underlining the pivotal role of the oligomeric status of IL37 in its anti-inflammatory action. Until now, two IL37 dimer structures have been deposited in PDB, reflecting a substantial difference in their dimer interfaces. Given this discrepancy, we analyzed the PDB structures of the IL37 dimer (PDB IDs: 6ncu, 5hn1) along with a AF2-multimer prediction by molecular dynamics (MD) simulations. Results showed that the 5hn1 and AF2-predicted dimers have the same interface and stably maintained their conformations throughout simulations, while the recent IL37 dimer (PDB ID: 6ncu) with a different interface did not, proposing a possible issue with the recent IL37 dimer structure (6ncu). Next, focusing on the stable dimer structures, we have identified five critical positions of V71/Y85/I86/E89/S114, three new positions compared to the literature, that would reduce dimer stability without affecting the monomer structure. Two quintuple mutants were tested by MD simulations and showed partial or complete dissociation of the dimer. Overall, the insights gained from this study reinforce the validity of the 5hn1 and AF2 multimer structures, while also advancing our understanding of the IL37 dimer interface through the generation of monomer-locked IL37 variants.
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Affiliation(s)
- Inci Sardag
- Bogazici University, Department of Molecular Biology and Genetics, Istanbul 34342, Turkey
| | - Zeynep Sevval Duvenci
- Acibadem Mehmet Ali Aydinlar University, Institute of Health Sciences, Department of Biostatistics and Bioinformatics, Istanbul 34752, Turkey
| | - Serkan Belkaya
- Bilkent University, Department of Molecular Biology and Genetics, Ankara 06800, Turkey
- Bilkent University, The National Nanotechnology Research Center (UNAM), Ankara 06800, Turkey
| | - Emel Timucin
- Acibadem Mehmet Ali Aydinlar University, Institute of Health Sciences, Department of Biostatistics and Bioinformatics, Istanbul 34752, Turkey
- Acibadem Mehmet Ali Aydinlar University, School of Medicine, Biostatistics and Medical Informatics, Istanbul 34752, Turkey
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Zhao Z, Yang T, Xiang G, Zhang S, Cai Y, Zhong G, Pu J, Shen C, Zeng J, Chen C, Huang B. A novel small RNA PhaS contributes to polymyxin B-heteroresistance in carbapenem-resistant Klebsiella pneumoniae. Emerg Microbes Infect 2024; 13:2366354. [PMID: 38979571 PMCID: PMC11238654 DOI: 10.1080/22221751.2024.2366354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 06/05/2024] [Indexed: 07/10/2024]
Abstract
In recent years, polymyxin has been used as a last-resort therapy for carbapenem-resistant bacterial infections. The emergence of heteroresistance (HR) to polymyxin hampers the efficacy of polymyxin treatment by amplifying resistant subpopulation. However, the mechanisms behind polymyxin HR remain unclear. Small noncoding RNAs (sRNAs) play an important role in regulating drug resistance. The purpose of this study was to investigate the effects and mechanisms of sRNA on polymyxin B (PB)-HR in carbapenem-resistant Klebsiella pneumoniae. In this study, a novel sRNA PhaS was identified by transcriptome sequencing. PhaS expression was elevated in the PB heteroresistant subpopulation. Overexpression and deletion of PhaS were constructed in three carbapenem-resistant K. pneumoniae strains. Population analysis profiling, growth curve, and time-killing curve analysis showed that PhaS enhanced PB-HR. In addition, we verified that PhaS directly targeted phoP through the green fluorescent protein reporter system. PhaS promoted the expression of phoP, thereby encouraging the expression of downstream genes pmrD and arnT. This upregulation of arnT promoted the 4-amino-4-deoxyL-arabinosaccharide (L-Ara4N) modification of lipid A in PhaS overexpressing strains, thus enhancing PB-HR. Further, within the promoter region of PhaS, specific PhoP recognition sites were identified. ONPG assays and RT-qPCR analysis confirmed that PhaS expression was positively modulated by PhoP and thus up-regulated by PB stimulation. To sum up, a novel sRNA enhancing PB-HR was identified and a positive feedback regulatory pathway of sRNA-PhoP/Q was demonstrated in the study. This helps to provide a more comprehensive and clear understanding of the underlying mechanisms behind polymyxin HR in carbapenem-resistant K. pneumoniae.
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Affiliation(s)
- Zhiwei Zhao
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Tingting Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Guoxiu Xiang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Shebin Zhang
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
| | - Yimei Cai
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
| | - Guosheng Zhong
- Department of Clinical Laboratory, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Jieying Pu
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
- Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, People’s Republic of China
| | - Cong Shen
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
- Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, People’s Republic of China
| | - Jianming Zeng
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
- Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, People’s Republic of China
| | - Cha Chen
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
- Department of Clinical Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, People’s Republic of China
| | - Bin Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
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Tayebi-Khorrami V, Rahmanian-Devin P, Fadaei MR, Movaffagh J, Askari VR. Advanced applications of smart electrospun nanofibers in cancer therapy: With insight into material capabilities and electrospinning parameters. Int J Pharm X 2024; 8:100265. [PMID: 39045009 PMCID: PMC11263755 DOI: 10.1016/j.ijpx.2024.100265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 06/07/2024] [Accepted: 06/22/2024] [Indexed: 07/25/2024] Open
Abstract
Cancer remains a major global health challenge, and despite available treatments, its prognosis remains poor. Recently, researchers have turned their attention to intelligent nanofibers for cancer drug delivery. These nanofibers exhibit remarkable capabilities in targeted and controlled drug release. Their inherent characteristics, such as a high surface area-to-volume ratio, make them attractive candidates for drug delivery applications. Smart nanofibers can release drugs in response to specific stimuli, including pH, temperature, magnetic fields, and light. This unique feature not only reduces side effects but also enhances the overall efficiency of drug delivery systems. Electrospinning, a widely used method, allows the precision fabrication of smart nanofibers. Its advantages include high efficiency, user-friendliness, and the ability to control various manufacturing parameters. In this review, we explore the latest developments in producing smart electrospun nanofibers for cancer treatment. Additionally, we discuss the materials used in manufacturing these nanofibers and the critical parameters involved in the electrospinning process.
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Affiliation(s)
- Vahid Tayebi-Khorrami
- Department of Pharmaceutics, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Pouria Rahmanian-Devin
- Department of Pharmaceutics, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Fadaei
- Department of Pharmaceutics, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jebraeel Movaffagh
- Department of Pharmaceutics, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Vahid Reza Askari
- Pharmacological Research Center of Medicinal Plants, Mashhad University of Medical Sciences, Mashhad, Iran
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Arshad N, Biswas N, Gill J, Kesari S, Ashili S. Drug delivery in leptomeningeal disease: Navigating barriers and beyond. Drug Deliv 2024; 31:2375521. [PMID: 38995190 PMCID: PMC11249152 DOI: 10.1080/10717544.2024.2375521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 06/27/2024] [Indexed: 07/13/2024] Open
Abstract
Leptomeningeal disease (LMD) refers to the infiltration of cancer cells into the leptomeningeal compartment. Leptomeninges are the two membranous layers, called the arachnoid membrane and pia mater. The diffuse nature of LMD poses a challenge to its effective diagnosis and successful management. Furthermore, the predominant phenotype; solid masses or freely floating cells, has altering implications on the effectiveness of drug delivery systems. The standard of care is the intrathecal delivery of chemotherapy drugs but it is associated with increased instances of treatment-related complications, low patient compliance, and suboptimal drug distribution. An alternative involves administering the drugs systemically, after which they must traverse fluid barriers to arrive at their destination within the leptomeningeal space. However, this route is known to cause off-target effects as well as produce subtherapeutic drug concentrations at the target site within the central nervous system. The development of new drug delivery systems such as liposomal cytarabine has improved drug delivery in leptomeningeal metastatic disease, but much still needs to be done to effectively target this challenging condition. In this review, we discuss about the anatomy of leptomeninges relevant for drug penetration, the conventional and advanced drug delivery methods for LMD. We also discuss the future directions being set by different clinical trials.
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Affiliation(s)
| | - Nupur Biswas
- Rhenix Lifesciences, Hyderabad, Telangana, India
- CureScience, San Diego, California, USA
| | - Jaya Gill
- CureScience, San Diego, California, USA
| | - Santosh Kesari
- Department of Translational Neurosciences, Pacific Neuroscience Institute and Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA
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Yang K, Shan X, Songru Y, Fu M, Zhao P, Guo W, Xu M, Chen H, Lu R, Zhang C. Network pharmacology integrated with experimental validation to elucidate the mechanisms of action of the Guizhi-Gancao Decoction in the treatment of phenylephrine-induced cardiac hypertrophy. PHARMACEUTICAL BIOLOGY 2024; 62:456-471. [PMID: 38773737 PMCID: PMC11123502 DOI: 10.1080/13880209.2024.2354335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 04/28/2024] [Indexed: 05/24/2024]
Abstract
CONTEXT The mechanisms of Traditional Chinese Medicine (TCM) Guizhi-Gancao Decoction (GGD) remain unknown. OBJECTIVE This study explores the mechanisms of GGD against cardiac hypertrophy. MATERIALS AND METHODS Network pharmacology analysis was carried out to identify the potential targets of GGD. In vivo experiments, C57BL/6J mice were divided into Con, phenylephrine (PE, 10 mg/kg/d), 2-chloroadenosine (CADO, the stable analogue of adenosine, 2 mg/kg/d), GGD (5.4 g/kg/d) and GGD (5.4 g/kg/d) + CGS15943 (a nonselective adenosine receptor antagonist, 4 mg/kg/d). In vitro experiments, primary neonatal rat cardiomyocytes (NRCM) were divided into Con, PE (100 µM), CADO (5 µM), GGD (10-5 g/mL) and GGD (10-5 g/mL) + CGS15943 (5 µM). Ultrasound, H&E and Masson staining, hypertrophic genes expression and cell surface area were conducted to verify the GGD efficacy. Adenosine receptors (ADORs) expression were tested via real-time polymerase chain reaction (PCR), western blotting and immunofluorescence analysis. RESULTS Network pharmacology identified ADORs among those of the core targets of GGD. In vitro experiments demonstrated that GGD attenuated PE-induced increased surface area (with an EC50 of 5.484 × 10-6 g/mL). In vivo data shown that GGD attenuated PE-induced ventricular wall thickening. In vitro and in vivo data indicated that GGD alleviated PE-induced hypertrophic gene expression (e.g., ANP, BNP and MYH7/MYH6), A1AR over-expression and A2aAR down-expression. Moreover, CADO exerts effects similar to GGD, whereas CGS15943 eliminated most effects of GGD. DISCUSSION AND CONCLUSIONS Our findings suggest the mechanism by which GGD inhibits cardiac hypertrophy, highlighting regulation of ADORs as a potential therapeutic strategy for HF.
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Affiliation(s)
- Kaijing Yang
- School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaoli Shan
- Public Laboratory Platform, School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yang Songru
- School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Mengwei Fu
- School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Pei Zhao
- Public Laboratory Platform, School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wei Guo
- Department of Pathology, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ming Xu
- Department of Physiology, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Huihua Chen
- School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Rong Lu
- School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Chen Zhang
- Department of Pathology, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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